Internal protein tags

ABSTRACT

Provided herein are substantially non-luminescent peptide/polypeptide tags that are inserted internally within a protein of interest or between N-terminal and C-terminal peptides/polypeptides. Interaction of the internally-inserted tag with a complement polypeptide/peptide that is also substantially non-luminescent results in the formation a bioluminescent reporter complex.

CROSS-REFERENCE TO RELATED APPLICATION

The present application is a divisional of U.S. patent application Ser. No. 14/852,096, filed Sep. 11, 2015, now U.S. Pat. No. 9,969,991, which claims priority to U.S. Provisional Patent Application Ser. No. 62/049,875 filed Sep. 12, 2014, each of which is hereby incorporated by reference in its entirety.

SEQUENCE LISTING

The text of the computer readable sequence listing filed herewith, titled “33980-403_SEQUENCE_LISTING_ST25”, created Oct. 15, 2020, having a file size of 2,025,000 bytes, is hereby incorporated by reference in its entirety.

FIELD

Provided herein are substantially non-luminescent peptide/polypeptide tags that are inserted internally within a protein of interest or between N-terminal and C-terminal peptides/polypeptides. Interaction of the internally-inserted tag with a complement polypeptide/peptide results in the formation a bioluminescent reporter complex.

BACKGROUND

Tagging of proteins with reporters or affinity tags is commonly used to analyze protein function and behavior. In general, genetic fusions are generated using either the C- or N-terminus of the protein of interest.

SUMMARY

Provided herein are substantially non-luminescent peptide/polypeptide tags that are inserted internally within a protein of interest or between N-terminal and C-terminal peptides/polypeptides. Interaction of the internally-inserted tag with a complement polypeptide/peptide results in the formation of a bioluminescent reporter complex.

In some embodiments provided herein are compositions, systems, methods etc. comprising a protein or polypeptide with an internal tag inserted therein. In some embodiments provided herein are compositions, systems, methods etc. comprising an internal tag inserted between C-terminal and N-terminal peptides/polypeptides. In certain embodiments, a structural complement sequence (or the internal tag) is also provided (e.g., free or as a fusion (e.g., internal or terminal)). In some embodiments, both the internal tag and the structural complement are substantially inactive (e.g., lacking enzymatic activity (e.g., substantially non-luminescent, etc.)). In some embodiments, the internal tag and the structural complement have high affinity for each other and form a complex (e.g., stable complex) when in solution together. In other embodiments, the internal tag and the structural complement have low affinity for each other and do not form a complex (e.g., stable complex) unless brought together by external factors/forces (e.g., interaction elements fused to the internal tag and structural complement). In some embodiments, a complex of the internal tag and the structural complement produces a detectable activity (e.g., luminescence in the presence of substrate).

In some embodiments, an internal fusion is provided. In some embodiments, an internal tag sequence (e.g., one that produces detectable activity when complexed with a structural complement) resides internally within the sequence of a protein or polypeptide sequence of interest. In some embodiments, an internal tag resides within the protein or polypeptide sequence of interest at a location that maintains: (i) the ability of the internal tag to form an active complex with a structural complement, and (ii) structural or activity characteristics of the protein or polypeptide of interest. In some embodiments, the structure or activity of one or more domains of interest of the protein or polypeptide of interest are uninterrupted by the presence of the internal tag within the sequence of the polypeptide or protein of interest. In some embodiments, the internal tag resides at a location within the protein of interest such that it is surface accessibly exposed on the surface of the protein of interest. In some embodiments, the internal tag resides at a loop of the protein of interest such that disruption to the structure and/or activity of the protein of interest is reduced/minimized.

In some embodiments, an internal tag sequence (e.g., one that produces detectable activity when complexed with a structural complement) resides internally between a C-terminal peptide/polypeptide and an N-terminal peptide/polypeptide. In some embodiments, an internal tag is linked to C-terminal and N-terminal peptides/polypeptides at locations that maintain: (i) the ability of the internal tag to form an active complex with a structural complement, and (ii) structural or activity characteristics of the C-terminal and N-terminal peptides/polypeptides.

In some embodiments, an internal tag and a complement peptide/polypeptide are fused to and/or inserted within separate domains of the same multi-domain protein. Upon folding of the protein, or a conformational change, activity from the complex of the internal tag and complement is detectable.

In some embodiments, methods of using an internal tag are provided. Some of the following embodiments are described for use with an internal tag and a protein of interest; however, whenever appropriate, they may also find use with an internal tag between N-terminal and C-terminal peptides/polypeptides.

In some embodiments, methods are provided for detecting the presence and/or location of a protein/polypeptide of interest using an internal tag and a structural complement that form an active complex upon association. In some embodiments, the presence and/or location in a sample (e.g., cell, subcellular location, in vitro sample, etc.) of a polypeptide with an internal tag is determined by adding a free structural complement having high affinity for the internal tag to the sample. Detection of the activity produced by complex formation indicates the presence and/or location of the protein/polypeptide of interest. In some embodiments, an active complex of an internal tag and a structural complement are detected in environments including, but not limited to: an in vitro sample, cell lysate, within living cells, within a living organism, etc.

In some embodiments, methods are provided for detecting interactions between a protein of interest and selected interaction partners (e.g., nucleic acids, peptides, proteins, polypeptides, small molecules, lipids, etc.) using an internal tag and a structural complement that form an active complex upon association. In some embodiments, the interaction of (i) a protein of interest with an internal tag and (ii) an interaction partner (e.g., nucleic acids, peptides, proteins, polypeptides, small molecules, lipids, etc.) linked to a structural complement having low affinity for the internal tag is detected upon formation of the active complex between the internal tag and the structural complement. In some embodiments, interactions are detected in environments including, but not limited to: an in vitro sample, cell lysate, within living cells, within a living organism, etc.

In some embodiments, methods are provided for detecting intramolecular interactions within a protein of interest by labeling the protein of interest with an internal tag and a complement peptide/polypeptide (internal or end-labeled with complement). A conformational change, folding, or other intramolecular interaction is detected by formation of a complex of the internal tag and the complement.

In some embodiments, the efficiency of complementation (and formation of an active complex and detectable luminescence) of an internal tag residing within a protein or polypeptide of interest and its structural complement is affected by one or more of: (i) conformational changes in the protein or polypeptide of interest (e.g., conformational changes that affect the accessibility of the internal tag to the structural complement), (ii) molecular interactions of the protein or polypeptide of interest (e.g., with a drug), and/or environmental changes (e.g., changes to conditions).

In some embodiments provided herein are compositions comprising a peptide and/or polypeptide tags that: (i) are not fragments of a preexisting protein, (ii) are substantially non-luminescent, (iii) are inserted internally within a protein of interest, and (iv) form a luminescent complex with a structurally complementary polypeptide and/or peptide. Also provided herein are luminescent complexes of the internal peptide and/or polypeptide tags with their complement polypeptide and/or peptide, and methods of generating an optically detectable bioluminescent signal upon formation of such complexes. In some embodiments provided herein are two or more substantially non-luminescent peptides and/or polypeptides, one or more of which are provided as internal protein tags that, when brought together, assemble into a bioluminescent complex. In some embodiments, a substantially non-luminescent peptide and/or polypeptide internal tag and its complement polypeptide/peptide assemble into a bioluminescent complex. In some embodiments, the complement peptide/polypeptide is also an internal tag. In other embodiments, the complement is a terminal (e.g., N-terminal of C-terminal) tag. In other embodiments, the complement is not associated with another peptide, polypeptide, or protein (e.g., free). In some embodiments, three or more substantially non-luminescent peptide and/or polypeptide units, one or more of which are internal protein tags assemble into a bioluminescent complex (e.g., ternary complex, tertiary complex, etc.). In some embodiments provided herein are technologies for detecting internally tagged proteins or polypeptides via the formation of a bioluminescent complex of the otherwise substantially non-luminescent internal tag and its substantially non-luminescent structural complement. In some embodiments, interactions between a protein of interest and another moiety (e.g., protein, peptide, nucleic acid, lipid, small molecule, etc.) are identified by detection of the formation of a bioluminescent complex between a substantially non-luminescent internal tag of the protein of interest and a substantially non-luminescent structural complement of the internal tag. In some embodiments, such compositions are provided in environments including, but not limited to: an in vitro sample, cell lysate, within living cells, within a living organism, etc.

In some embodiments, interactions between different regions of a protein, or domains of a multi-domain protein, are detected by labeling the different regions/domains with an internal tag and complement. Activity from the complex of the internal tag and complement indicates intra-protein interactions (e.g., conformational change, folding, etc.).

In some embodiments, the complex of a substantially non-luminescent internal tag and its substantially non-luminescent structural complement catalyzes a chemical reaction of an appropriate substrate into a high energy state, and light is emitted. In some embodiments, a bioluminescent complex of an internal protein tag and its structural complement exhibits luminescence in the presence of substrate (e.g., coelenterazine, furimazine, etc.).

Although the embodiments described herein primarily describe and refer to the formation of a luminescent complex (e.g., comprising at least one substantially non-luminescent tag and its substantially non-luminescent complement) complementary, it is noted that the present technology can equally be applied to other detectable attributes (e.g., other enzymatic activities, generation of a fluorophore, generation of a chromophore, etc.). The embodiments described herein relating to luminescence should be viewed as applying to internal tags that are substantially non-enzymatically active amino acid chains (e.g., peptides and/or polypeptides that are not fragments of a preexisting protein) and their structurally complementary polypeptide/peptide that also lack a specified detectable activity (e.g., enzymatic activity), and the enzymatically active complexes thereof. Provided herein are methods of generating a detectable activity (e.g., an enzymatic activity) upon association of a substantially non-enzymatically active, internal tag and its substantially non-enzymatically active complement peptide/polypeptide.

The invention is further directed to assays for the detection of molecular interactions (e.g., transient association, stable association, complex formation, etc.) between a protein (or polypeptide) of interest and another moiety (e.g., peptide, polypeptide, protein, nucleic acid, small molecule etc.) by inserting an internal tag into the protein of interest and tagging the other moiety (e.g., internally labeled, terminally labeled, etc.) with the structural complement of the internal tag, wherein no signal (e.g., substantially no signal) is produced in the absence of the molecular interaction between the protein of interest and the other moiety, but a detectable (e.g., bioluminescent) complex of the internal tag and its complement is produced upon interaction of the protein of interest and the other moiety. In such embodiments, assembly of the bioluminescent complex is operated by the molecular interaction of the protein of interest and the other moiety. If the protein of interest and the other moiety engage in a sufficiently stable interaction, the bioluminescent complex of the internal tag and its complement forms, and a bioluminescent signal is generated. If the protein of interest and the other moiety fail to engage in a sufficiently stable interaction, the bioluminescent complex does not form, or only weakly forms, and a bioluminescent signal is not generated or is substantially reduced (e.g., substantially undetectable, essentially not detectable, differentially detectable as compared to a stable control signal, etc.). In some embodiments, the magnitude of the detectable bioluminescent signal is proportional (e.g., directly proportional) to the amount, strength, favorability, and/or stability of the molecular interactions between the protein of interest and the other moiety.

In some embodiments, provided herein are internal tags comprising an amino acid sequence having less than 100% (e.g., 20% . . . 30% . . . 40% . . . 50% . . . 60% . . . 70% . . . 80%, 90% or more) sequence identity with SEQ ID NO: 2, wherein a detectable bioluminescent signal is produced when the peptide contacts a complement polypeptide of SEQ ID NO: 440. In some embodiments, provided herein are internal tags comprising an amino acid sequence having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 2, wherein a detectable bioluminescent signal is produced when the peptide contacts a structurally complementary polypeptide of SEQ ID NO: 440. In some embodiments, a detectable bioluminescent signal is produced when the internal tag contacts a polypeptide having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 440. In certain embodiments, the detectable bioluminescent signal is produced, or is substantially increased, when the internal tag associates with the polypeptide comprising or consisting of SEQ ID NO: 440, or a portion thereof. Although not limited to these sequences, the peptide amino acid sequence may be selected from amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365. In some embodiments, polypeptides are provided that comprise an above described internal tag inserted into a protein or polypeptide of interest (e.g., not on the C- or N-terminus of the protein or polypeptide). In some embodiments, a structural complement of the internal tag is provided alone or as a tag (e.g., internal or terminal) of another moiety (e.g., protein, peptide, polypeptide, nucleic acid, lipid, small molecule, etc.). In certain embodiments, bioluminescent complexes are provided that comprise: (a) a first polypeptide having an internal tag (e.g., not located at the N- of C-terminus); and (b) a peptide or polypeptide comprising a structural complement of the internal tag; wherein, when associated, the internal tag and its structural complement emit a detectable bioluminescent signal in the present of an appropriate substrate. In some embodiments, the internal tag comprises an amino acid sequence having less than 100% and greater than 30% sequence identity with SEQ ID NO: 2 and a detectable bioluminescent signal is produced when the internal tag contacts a structurally complementary polypeptide of SEQ ID NO: 440 in the presence of substrate.

In some embodiments provided herein are internal tags comprising an amino acid sequence having less than 100% sequence identity with SEQ ID NO: 440, wherein a detectable bioluminescent signal is produced when the internal tag contacts a peptide of SEQ ID NO: 2 in the presence of substrate. In some embodiments, the present invention provides internal tags comprising an amino acid sequence having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 440, wherein a detectable bioluminescent signal is produced when the internal tag contacts a peptide of SEQ ID NO: 2. In some embodiments, a detectable bioluminescent signal is produced when the internal tag contacts a peptide having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 2. Although not limited to such sequences, the internal tag sequence may be selected from one of the amino acid sequences of SEQ ID NOS: 441-2156. In some embodiments, a detectable bioluminescent signal is produced when the internal tag associates with a peptide of SEQ ID NO: 2 in the presence of appropriate substrate. In certain embodiments, bioluminescent complexes are provided that comprise: (a) a first polypeptide having an internal tag (e.g., not located at the N- of C-terminus); and (b) a peptide or polypeptide comprising a structural complement of the internal tag; wherein, when associated, the internal tag and its structural complement emit a detectable bioluminescent signal in the present of an appropriate substrate. In some embodiments, the internal tag comprises an amino acid sequence having less than 100% and greater than 30% sequence identity with SEQ ID NO: 440 and a detectable bioluminescent signal is produced when the internal contacts a structurally complementary peptide of SEQ ID NO: 2 in the presence of substrate.

In some embodiments, provided herein are nucleic acids (e.g., DNA, RNA, etc.), oligonucleotides, vectors, etc., that code for any of the peptides, polypeptides (e.g., comprising internal tags, comprising terminal tags, etc.), proteins (e.g., comprising internal tags, comprising terminal tags, etc.), fusion proteins, etc., described herein. In some embodiments, a nucleic acid comprising or consisting of one of the nucleic acid sequences of SEQ ID NOS: 3-438 and 2162-2365 (e.g., coding peptide internal tags, coding for peptide structural complements) and/or SEQ ID NOS 441-2156 (e.g., coding polypeptide internal tags, coding for polypeptide structural complements) are provided. In some embodiments, other nucleic acid sequences coding for amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365 and/or SEQ ID NOS 441-2156 are provided.

In certain embodiments provided herein are bioluminescent complexes comprising: (a) a first polypeptide having an internal (e.g., not at the N- or C-terminus) tag comprising an amino acid sequence having less than 100% sequence identity (e.g., <99%, <95%, <90%, <80%, <70%, <60%, <50%, etc.) with SEQ ID NO: 2; and (b) a second polypeptide comprising an amino acid sequence (e.g., internally or terminally) having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 440, wherein the bioluminescent complex exhibits detectable bioluminescence in the presence of substrate. In certain embodiments, provided herein are bioluminescent complexes comprising: (a) a polypeptide comprising an internal tag comprising an amino acid sequence having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 2; and (b) a polypeptide comprising an amino acid sequence having less than 100% and greater than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with SEQ ID NO: 440, wherein the bioluminescent complex exhibits detectable bioluminescence in the presence of substrate.

In various embodiments, bioluminescent complexes are provided that comprise: (a) a first amino acid sequence comprising an internal tag sequence that is not a fragment of a preexisting protein; and (b) a second amino acid sequence comprising an amino acid sequence that is not a fragment of a preexisting protein, wherein the bioluminescent complex exhibits detectable bioluminescence when the first amino acid sequence and the second amino acid sequence are associated.

In some embodiments, interacting polypeptides are provided, wherein the first polypeptide comprises an internal tag (e.g., an amino acid sequence inserted at a position within its sequence (e.g., not at the N- or C-terminus)), and wherein the second polypeptide comprises a structural complement tag (e.g., an internally- or terminally-located amino acid sequence that is structurally complementary to the internal tag). Upon interaction of the first and second polypeptides, the internal tag and the structural complement tag associate to form a bioluminescent complex. In some embodiments, interaction of the interacting polypeptides is assessed based on the bioluminescence of the bioluminescent complex. In certain embodiments, interactions (e.g., non-covalent interactions (e.g., hydrogen bonds, ionic bonds, van der Waals forces, hydrophobic interactions, etc.), covalent interactions (e.g., disulfide bonds), etc.) between the internal tag and the structural complement tag do not result in significant bioluminescent complex formation in the absence of the interacting polypeptides. In some embodiments, such a system exists (e.g., is expressed) within a cell.

In some embodiments provided herein are bioluminescent complexes comprising: (a) a first substantially non-luminescent element inserted within a polypeptide sequence; and (b) a second substantially non-luminescent element (e.g., free, attached to a polypeptide (e.g., internally or terminally) attached to a molecular entity (e.g., small molecule, etc.), etc.) wherein each non-luminescent element is not a fragment of a preexisting protein.

Various embodiments described herein provide methods of detecting an interaction between a first amino acid sequence and a second amino acid sequence comprising, for example, the steps of: (a) inserting an internal tag within the first amino acid sequence and attaching a complement sequence (e.g., internally or terminally) to the second amino acid sequence, wherein the internal tag and complement sequences are not fragments of a preexisting protein, wherein a complex of the internal tag and the complement sequence emits a detectable bioluminescent signal (e.g., substantially increased bioluminescence relative to the internal tag and the complement sequence separately), wherein the interactions (e.g., non-covalent) between the internal tag and complementary sequence are insufficient to form, or only weakly form, a complex in the absence of additional stabilizing and/or aggregating conditions, and wherein an interaction between the first amino acid sequence and the second amino acid sequence provides the additional stabilizing and/or aggregating forces to produce a complex of the internal tag and the complement sequence; (b) placing the tagged first and second amino acid sequences of step (a) in conditions to allow for interactions between the first amino acid sequence and the second amino acid sequence to occur; and (c) detecting the bioluminescent signal emitted by the complex of the internal tag and complement sequence in the presence of appropriate substrate, wherein detection of the bioluminescent signal indicates an interaction between the first amino acid sequence and the second amino acid sequence. In some embodiments, the first amino acid sequence and the internal tag comprise an internal fusion. In some embodiments, the second amino acid sequence and the complement sequence comprise an internal fusion or a traditional fusion. In some embodiments, the first internal fusion protein (e.g., comprising an internal tag) and the second fusion protein (e.g., comprising a complement sequence) further comprise linkers between the fused elements. In certain embodiments, the fusion proteins are expressed from nucleic acids encoding said fusion proteins. In some embodiments, a single vector comprises both fusion proteins. In other embodiments, first and second fusion proteins are expressed from separate vectors.

In some embodiments provided herein are polypeptides comprising an N-terminal segment, a C-terminal segment, and an internal tag, wherein the internal tag comprises an amino acid sequence having less than 100% and greater than 30% sequence identity with SEQ ID NO: 2 inserted within a protein of interest; wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide of SEQ ID NO: 440. In some embodiments, both the N-terminal segment and the C-terminal segment are at least 20 amino acids in length. In some embodiments, the N-terminal segment and/or the C-terminal segment are at least 50 amino acids in length. In some embodiments, the internal tag exhibits enhancement of one or more traits compared to a peptide of SEQ ID NO: 2, wherein the traits are selected from: affinity for the polypeptide of SEQ ID NO: 440, expression, intracellular solubility, intracellular stability, and bioluminescent activity when combined with the polypeptide of SEQ ID NO: 440. In some embodiments, the internal tag is selected from the peptides of Table 1. In some embodiments, the N-terminal segment and the C-terminal segment, if directly linked in the absence of the internal tag, comprise the sequence of a first protein of interest. In some embodiments, a nucleic acid is provided comprising a sequence coding for the internally tagged polypeptide. In some embodiments, a bioluminescent complex is provided comprising: (a) the internally tagged polypeptide; and (b) a second polypeptide comprising a complement polypeptide having less than 100% and greater than 30% sequence identity with SEQ ID NO: 440. In some embodiments, the internal tag and the complement polypeptide have low affinity for each other. In some embodiments, the second polypeptide is a fusion with a second protein of interest. In some embodiments, the fusion is an internal fusion or a traditional fusion. In some embodiments, the second protein of interest has an affinity for all or a portion of the N-terminal segment and/or the C-terminal segment. In some embodiments, the affinity may be altered by a structural modification to the first or second protein (e.g., a post-translational modification), or both, or by interaction with a third molecule (e.g., a drug, a nucleic acid, a protein, etc.). In some embodiments, the second polypeptide is linked to a molecule of interest. In some embodiments, all or a portion of the N-terminal segment and/or the C-terminal segment has an affinity for the molecule of interest. In some embodiments, a bioluminescent complex further comprises a coelenterazine substrate (e.g., furimazine). In some embodiments, the internal tag and the complement polypeptide have high affinity for each other. In some embodiments, the second polypeptide is not a fusion polypeptide or linked to a molecule of interest. In some embodiments, the complement polypeptide is selected from the peptides of Table 2.

In some embodiments provided herein are polypeptides comprising an N-terminal segment, a C-terminal segment, and an internal tag, wherein the internal tag comprises an amino acid sequence having less than 100% and greater than 30% sequence identity with SEQ ID NO: 440 inserted within a protein of interest; wherein a detectable bioluminescent signal is produced in the presence of a substrate when the detection peptide contacts a polypeptide of SEQ ID NO: 2. In some embodiments, both the N-terminal segment and the C-terminal segment are at least 20 amino acids in length. In some embodiments, the N-terminal segment and/or the C-terminal segment are at least 50 amino acids in length. In some embodiments, the internal tag exhibits enhancement of one or more traits compared to a peptide of SEQ ID NO: 440, wherein the traits are selected from: affinity for the polypeptide of SEQ ID NO: 2, expression, intracellular solubility, intracellular stability, and bioluminescent activity when combined with the polypeptide of SEQ ID NO: 2. In some embodiments, the internal tag is selected from the peptides of Table 2. In some embodiments, the N-terminal segment and the C-terminal segment, if directly linked in the absence of the internal tag, comprise the sequence of a first protein of interest. In some embodiments, a nucleic acid is provided comprising a sequence coding for the internally tagged polypeptide. In some embodiments, a bioluminescent complex is provided comprising: (a) the internally tagged polypeptide; and (b) a complement peptide having less than 100% and greater than 30% sequence identity with SEQ ID NO: 2. In some embodiments, the internal tag and the complement peptide have low affinity for each other. In some embodiments, the complement peptide is a fusion with a second protein of interest. In some embodiments, the fusion is an internal fusion or a traditional fusion. In some embodiments, the second protein of interest has an affinity for all or a portion of the N-terminal segment and/or the C-terminal segment. In some embodiments, the affinity may be altered by a structural modification to the first or second protein (e.g., a post-translational modification), or both, or by interaction with a third molecule (e.g., a drug, a nucleic acid, a protein, etc.). In some embodiments, the complement peptide is linked to a molecule of interest. In some embodiments, all or a portion of the N-terminal segment and/or the C-terminal segment has high affinity for the molecule of interest. In some embodiments, the bioluminescent complex further comprises a coelenterazine substrate. In some embodiments, the internal tag and the complement peptide have high affinity for each other. In some embodiments, the complement peptide is selected from the peptides of Table 1. In some embodiments, the complement peptide is not a fusion polypeptide or linked to a molecule of interest.

In some embodiments provided herein are methods of detecting an interaction between a first amino acid sequence and a second amino acid sequence comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide of SEQ ID NO: 440; (b) creating a second fusion of the second amino acid sequence and a complement polypeptide, wherein the complement polypeptide has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the complement polypeptide contacts a peptide of SEQ ID NO: 2; (c) placing the internal fusion, second fusion, and a coelenterazine substrate in conditions that allow for a possible interaction to occur between the first amino acid sequence and the second amino acid sequence; and (d) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates an interaction between the first amino acid sequence and the second amino acid sequence. In some embodiments, the interaction is detected in living cells or organisms by detecting the bioluminescence signal emitted by the cells or organism. In some embodiments, an alteration in the interaction resulting from an alteration of the environment of the cells is detected by detecting a difference in the emitted bioluminescent signal relative to control cells absent the altered environment. In some embodiments, the altered environment is the result of adding or removing a molecule from the culture medium (e.g., a drug). In some embodiments, the second fusion is an internal fusion or a traditional fusion. In some embodiments, the internal fusion is expressed from a first nucleic acid sequence coding for the first amino acid sequence and the internal tag, and the second fusion is expressed from a second nucleic acid sequence coding for the second amino acid sequence and the complement polypeptide. In some embodiments, a single vector comprises the first nucleic acid sequence and the second nucleic acid sequence. In some embodiments, the first nucleic acid sequence and the second nucleic acid sequence are on separate vectors. In some embodiments, steps (a) and (b) comprise expressing the internal fusion and second fusion within a cell.

In some embodiments, provided herein are methods of detecting an interaction between a first amino acid sequence and a second amino acid sequence comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2; (b) creating a second fusion of the second amino acid sequence and a complement peptide, wherein the complement peptide has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the complement peptide contacts a polypeptide of SEQ ID NO: 2; (c) placing the internal fusion, second fusion, and a coelenterazine substrate in conditions that allow for a possible interaction to occur between the first amino acid sequence and the second amino acid sequence; and (d) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates an interaction between the first amino acid sequence and the second amino acid sequence. In some embodiments, the second fusion is an internal fusion or a traditional fusion. In some embodiments, the internal fusion is expressed from a first nucleic acid sequence coding for the first amino acid sequence and the internal tag, and the second fusion is expressed from a second nucleic acid sequence coding for the second amino acid sequence and the complement peptide. In some embodiments, a single vector comprises the first nucleic acid sequence and the second nucleic acid sequence. In some embodiments, the first nucleic acid sequence and the second nucleic acid sequence are on separate vectors. In some embodiments, steps (a) and (b) comprise expressing the internal fusion and second fusion within a cell.

In some embodiments provided herein are methods of detecting a target polypeptide in a sample comprising: (a) creating an internal fusion by inserting an internal tag into the target polypeptide, such that said internal tag is neither at the N-terminus not the C-terminus of the target polypeptide, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2; (b) adding to said sample: (i) a complement peptide that has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, and (ii) a coelenterazine substrate; and (c) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates the presence of the target polypeptide in the sample. In some embodiments, the sample comprises a cell. In some embodiments, step (a) comprises expressing said internal fusion in said cell. In some embodiments, step (b)(i) comprises said complement peptide in said cell.

In some embodiments provided herein are methods of detecting a target polypeptide in a sample comprising: (a) creating an internal fusion by inserting an internal tag into the target polypeptide, such that said internal tag is neither at the N-terminus not the C-terminus of the target polypeptide, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 440; (b) adding to said sample: (i) a complement polypeptide that has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, and (ii) a coelenterazine substrate; and (c) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates the presence of the target polypeptide in the sample. In some embodiments, the sample comprises a cell. In some embodiments, step (a) comprises expressing said internal fusion in said cell. In some embodiments, step (b)(i) comprises said complement polypeptide in said cell.

In some embodiments provided herein are detection reagents comprising: (a) a complement polypeptide comprising an amino acid sequence having less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, wherein a detectable bioluminescent signal is produced, in the presence of a substrate, when the polypeptide contacts a peptide of SEQ ID NO: 2, and (b) a substrate for a bioluminescent complex produced by said polypeptide and a peptide of SEQ ID NO: 2.

In some embodiments provided herein are detection reagents comprising: (a) a complement peptide comprising an amino acid sequence having less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, wherein a detectable bioluminescent signal is produced, in the presence of a substrate, when the peptide contacts a polypeptide of SEQ ID NO: 440, and (b) a substrate for a bioluminescent complex produced by said peptide and a polypeptide of SEQ ID NO: 440.

In certain embodiments, an internal tag and/or structural complement comprises or consists of an amino acid having 100% sequence identity with SEQ ID NO: 2 or SEQ ID NO: 440. In some embodiments, such internal tags and structural complements find use in any embodiments described herein and with any other peptide or polypeptide sequences described herein.

In some embodiments provided herein are methods of detecting alteration of an interaction between a first amino acid sequence and a second amino acid sequence by an agent comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide of SEQ ID NO: 440; (b) creating a second fusion of the second amino acid sequence and a complement polypeptide, wherein the complement polypeptide has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the complement polypeptide contacts a peptide of SEQ ID NO: 2; (c) placing the internal fusion, second fusion, and a coelenterazine substrate in conditions that allow for a possible interaction to occur between the first amino acid sequence and the second amino acid sequence;

(d) detecting, if present, a bioluminescent signal emitted; (e) adding the agent to the internal fusion, second fusion, and a coelenterazine substrate; (f) detecting, if present, a bioluminescent signal emitted; and (g) comparing the bioluminescent signals of steps (d) and (f), wherein change in bioluminescent signal from step (d) to step (f) indicates alteration of the interaction between the first amino acid sequence and the second amino acid sequence by the agent. In some embodiments, steps (a) and (b) comprise expressing the internal fusion and second fusion within a cell. In some embodiments, the agent is a peptide or small molecule. In some embodiments, the agent is an inhibitor of the interaction, wherein reduced interaction is detected by a decrease in the bioluminescent signal. In some embodiments, the agent is an activator of the interaction, wherein increased interaction is detected by an increase in the bioluminescent signal.

In some embodiments, provided herein are methods of detecting alteration of an interaction between a first amino acid sequence and a second amino acid sequence by an agent comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2; (b) creating a second fusion of the second amino acid sequence and a complement polypeptide, wherein the complement peptide has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the complement polypeptide contacts a polypeptide of SEQ ID NO: 440; (c) placing the internal fusion, second fusion, and a coelenterazine substrate in conditions that allow for a possible interaction to occur between the first amino acid sequence and the second amino acid sequence; (d) detecting, if present, a bioluminescent signal emitted; (e) adding the agent to the internal fusion, second fusion, and a coelenterazine substrate; (f) detecting, if present, a bioluminescent signal emitted; and (g) comparing the bioluminescent signals of steps (d) and (f), wherein change in bioluminescent signal from step (d) to step (f) indicates alteration of the interaction between the first amino acid sequence and the second amino acid sequence by the agent. In some embodiments, steps (a) and (b) comprise expressing the internal fusion and second fusion within a cell. In some embodiments, the agent is a peptide or small molecule. In some embodiments, the agent is an inhibitor of the interaction, wherein reduced interaction is detected by a decrease in the bioluminescent signal. In some embodiments, the agent is an activator of the interaction, wherein increased interaction is detected by an increase in the bioluminescent signal.

In some embodiments provided herein are methods of detecting an alteration in the structural conformation of a first amino acid sequence by an agent comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 2, wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide of SEQ ID NO: 440, wherein a first structural conformation of the first amino acid sequence alters access to the internal tag relative to a second structural conformation of the first amino acid sequence; (b) placing the internal fusion and either (i) a complement polypeptide having less than 100% and greater than 30% sequence identity with SEQ ID NO: 440 or (ii) a second fusion of a second amino acid sequence and the complement polypeptide in the presence of a coelenterazine substrate; (c) detecting, if present, a bioluminescent signal emitted; (d) adding the agent to the internal fusion, second fusion, and a coelenterazine substrate; (e) detecting, if present, a bioluminescent signal emitted; and (f) comparing the bioluminescent signals of steps (c) and (e), wherein change in bioluminescent signal from step (c) to step (e) indicates alteration of the conformation of the first amino acid sequence by the agent. In some embodiments, inducing a conformational change is selected from: adding a protease that cleave a portion of the first amino acid sequence, addition an agent that binds to the first amino acid sequence, and altering the assay conditions.

In some embodiments provided herein are methods of detecting an alteration in the structural conformation of a first amino acid sequence by an agent comprising (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 30% sequence identity with SEQ ID NO: 440, wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2, wherein a first structural conformation of the first amino acid sequence alters access to the internal tag relative to a second structural conformation of the first amino acid sequence; (b) placing the internal fusion and either (i) a complement peptide having less than 100% and greater than 30% sequence identity with SEQ ID NO: 2 or (ii) a second fusion of a second amino acid sequence and the complement peptide in the presence of a coelenterazine substrate; (c) detecting, if present, a bioluminescent signal emitted; (d) adding the agent to the internal fusion, second fusion, and a coelenterazine substrate; (e) detecting, if present, a bioluminescent signal emitted; and (f) comparing the bioluminescent signals of steps (c) and (e), wherein change in bioluminescent signal from step (c) to step (e) indicates alteration of the conformation of the first amino acid sequence by the agent. In some embodiments, inducing a conformational change is selected from: adding a protease that cleaves a portion of the first amino acid sequence, adding an agent that binds to the first amino acid sequence, and altering the assay conditions.

In some embodiments provided herein are polypeptides comprising an N-terminal segment, a C-terminal segment, and two or more internal tags, wherein the internal tags comprise amino acid sequences having less than 100% and greater than 30% sequence identity with SEQ ID NO: 2 inserted within a protein of interest; wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when one or more of the internal tags contact a polypeptide of SEQ ID NO: 440. In some embodiments, the two or more internal tags are two internal tags (e.g., tandem tags). In some embodiments, the two or more internal tags are directly connected to one another. In some embodiments, the two or more internal tags are separated by one or more linkers (e.g., peptide linker). In some embodiments, the two or more internal tags are inserted at a single location within the protein or polypeptide of interest. In some embodiments, the two or more internal tags are inserted at two or more locations within the protein or polypeptide of interest. In some embodiments, the two or more internal tags comprise identical amino acid sequences. In some embodiments, the two or more or the two or more internal tags comprise non-identical amino acid sequences. In some embodiments, the two or more internal tags have amino acid substitutions that may or may not have an impact on affinity with a complement sequence, but that change the overall charge of the internal tag or tandem tags to be either more charged or closer to neutral.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic depiction of an exemplary embodiment in which an internal tag (e.g., NLpep or NLpoly) is inserted into a first protein of interest (POI 1) as an internal loop, and a complement sequence (e.g., NLpep or NLpoly) is fused terminally to a second protein of interest (POI 2). The internal tag and complement sequence have low affinity for each other, such that they are ineffective in forming a complex (e.g., produce an undetectable or negligible amount of complex) in the absence of external forces. Although the internal tag and complement sequence are separately substantially non-luminescent, upon interaction of POI 1 and POI 2, a bioluminescent complex is formed between the internal tag and complement sequence.

FIG. 2 shows a schematic depiction of an exemplary embodiment in which an internal tag (e.g., NLpep or NLpoly) is inserted into a first protein of interest (POI 1), and a free complement sequence (e.g., NLpep or NLpoly) is provided. In this example, the internal tag is placed in a position that is accessible only after the protein of interest undergoes a conformational change that allows the internal tag to be accessible by the complement sequence. The internal tag and complement sequence have high affinity for each other such that a complex forms when the internal tag and complement sequence associate. A bioluminescent complex is then formed between the internal tag and complement sequence when they are present in the same sample.

FIG. 3 shows a schematic depiction of an exemplary embodiment in which an internal tag (e.g., NLpep or NLpoly) and its structural complement are inserted/fused to a polypeptide of interest (POI 1). In this example, the internal tag is placed in a position that is accessible only after the protein of interest undergoes a conformational change that allows the internal tag to be accessible by the complement sequence. The internal tag and complement sequence have high affinity for each other such that a complex forms when the internal tag and complement sequence associate. A bioluminescent complex is then formed between the internal tag and complement sequence when they are present in the same sample.

FIG. 4 shows the results of a representative experiment demonstrating structural complementation of the high affinity NLpeptide86 internal tag inserted into the HALOTAG protein (Promega Corp) and NLpoly11S. In this experiment, HeLa cells were transfected with the expression constructs for the indicated constructs. The cells were incubated for 24 hours. Luminescence of each sample was measured following addition of the NANOLUC substrate furimazine

FIG. 5 shows an image demonstrating function of a HALOTAG protein (Promega Corp) having the high affinity NLpeptide86 inserted therein.

FIG. 6 depicts a schematic of how the assay components are used to screen for antibody binding to target protein by way of antibody driven NANOLUC bioluminescence complementation between NLpoly11S-fused protein G and internally tagged NLpep114 target protein. The Target, containing an internal pep114 tag, is expressed in mammalian cell culture with an IL6 signal peptide (SP). The SP directs the Target to the secretion pathway. The Target can be assayed in the media (+/−) cells. In the example, a purified preparation of the Large Bit (11S-protein G fusion protein) and Test Antibody are added directly to the mammalian cell culture. The protein G domain of the Large Bit binds to the Fc region of the Test Antibody between the Heavy Chain Constant Domains 2 and 3. If the Test Antibody binds to the Target, the Large and Small Bits can come together to form an active luminesent complex that is detected by furimazine.

FIG. 7 depicts the target protein of interest configurations with the NLpep114 tag either unencumbered on the C-terminus serving as a control, or placed between polypeptides as an internal tag. VEGFA is shown here as this target protein serves in the proof of concept data. Any soluble target protein of interest can be used. HT (HALOTAG), 114 (Small Bit), VEGF (Vascular Endothelial Growth Factor), FLAG (FLAG octapeptide). ATG1915: Control Target with a terminal Small Bit; ATG 1917: Experimental Target with the Small Bit between two large domains; and ATG 1946: Experimental Target with the Small Bit between one large and one small domain.

FIG. 8 shows target antibody specific NANOLUC bioluminescence complementation by the detection of anti-VEGFA specific antibody binding to the NLpep114 tagged VEGFA target proteins as determined by an increase in bioluminescence in an antibody concentration dependent manner. This increase in bioluminescence was antibody:target specific as isotype controls did not produce light (not shown).

FIG. 9 shows target antibody specific NANOLUC bioluminescence complementation as fold signal/background. The signal window of detection of anti-VEGFA specific antibody binding to the NLpep114 tagged VEGFA target proteins as determined by the increase in bioluminescence in the presence of antibody over background of assay components without antibody present. The signal over background in RLU was calculated from data obtained in FIG. 8 and found to increase from 75-450 fold in response to increasing anti-VEGFA antibody over the concentration range used.

FIG. 10 demonstrates the affinity of the antibody for the target is unchanged by the position of NLpep114, as shown by anti-VEGFA antibody relative affinity through bioluminescence complementation dose response. The EC₅₀ values for the three VEGFA target constructs are shown as calculated off the dose response curves generated in FIG. 8.

FIG. 11 depicts the schematic of how the assay components are used to quantify endogenous target protein along with prophetic data analysis by way of endogenous target protein competition with NLpep114 tagged target protein and antibody driven NANOLUC bioluminescence complementation between NLpoly11S-fused protein G and internally tagged NLpep114 target protein. Assay components configured to allow for quantitation of endogenous target protein of interest. Using the same target protein pep114 fusions and 11S-protein G fusions, one can quantitate the amount of endogenous target protein through binding competition resulting in a decrease in signal as endogenous target protein increases.

FIG. 12 depicts a schematic representation and sequence of the 114 tandem peptide (SEQ ID NO: 2581) used for internal tagging.

FIG. 13 depicts a schematic representation of FKBP/Frb fusion proteins. Shown are fusions of NLpoly11S fused to the C- or N-terminus of either FKBP or Frb, and the integration of the internal tag (NLpep114 tandem peptide=2×NLpep114) at different position within FKBP or Frb. The position of the integration site of the internal tag is indicated by the flanking amino acid positions of the host protein (e.g., AA12/13 indicates integration of 2×NLpep114 between amino acid 12 and 13 of FKBP).

FIG. 14 demonstrates rapamycin-induced protein-protein interaction of FKBP/Frb using the internal tagging described herein. Position of the NLpep114 tandem peptide is indicated as C-terminal (C-114) or by the N-terminally flanking amino acid of the host protein (e.g. 12 indicates integration between AA12 and 13 within FKBP).

FIG. 15 demonstrates the conversion of the results shown in FIG. 15 into a relative change between untreated and rapamycin-treated sample (response ratio). The response ratio is calculated using the equation: response ratio=RLUrapamycin/RLUuntreated.

FIG. 16 demonstrates dose-dependent induction of the FKBP/Frb interaction by rapamycin using the internal tagging described herein.

FIG. 17 demonstrates kinetic measurement of the rapamycin-induced FKBP/Frb interaction using the internal tagging described herein. All results are shown using Relative Light Units (RLU) as unit of measurement plotted either on a logarithmic (left) or linear scale (right).

FIG. 18 demonstrates a normalized representation of results shown in FIG. 17 (left graph). For normalization, minimum and maximum values obtained for each individual trace were used as reference points (0% and 100% respectively).

DEFINITIONS

As used herein, the term “internal tag” refers to a peptide or polypeptide sequence that is inserted within another polypeptide or protein (e.g., not at the N- or C-terminus). The internal tag may provide one or more characteristics of detection, isolation, localization, association, etc. to the peptide or polypeptide sequence within which it is inserted. An internal tag may either be directly connected to the N- and C-terminal portions of the polypeptide or protein or may be connected by one or more linkers. In some embodiments, the linkers themselves may provide a functionality.

As used herein, the term “substantially” means that the recited characteristic, parameter, and/or value need not be achieved exactly, but that deviations or variations, including for example, tolerances, measurement error, measurement accuracy limitations and other factors known to those of skill in the art, may occur in amounts that do not preclude the effect the characteristic was intended to provide. A characteristic or feature that is substantially absent (e.g., substantially non-luminescent) may be one that is within the noise, beneath background, or below the detection capabilities of the assay being used.

As used herein, the term “bioluminescence” refers to production and emission of light by a chemical reaction catalyzed by, or enabled by, an enzyme, protein, protein complex, or other biomolecule (e.g., bioluminescent complex). In typical embodiments, a substrate for a bioluminescent entity (e.g., bioluminescent protein or bioluminescent complex) is converted into a high-energy reaction product by the bioluminescent entity; the reaction product subsequently emits light as it converts to a more stable form.

As used herein the term “complementary” refers to the characteristic of two or more structural elements (e.g., peptide, polypeptide, nucleic acid, small molecule, etc.) of being able to hybridize, dimerize, or otherwise form a complex with each other. For example, a “complementary peptide and polypeptide” are capable of coming together to form a complex. Complementary elements may require assistance to form a stable complex (e.g., from interaction elements), for example, to place the elements in the proper conformation for complementarity, to co-localize complementary elements, to lower interaction energy for complementary, etc. In some embodiments, a “complement sequence”, a “complement”, or a “structural complement” is an amino acid sequence that is the structural complement of another sequence (e.g., of an internal tag).

As used herein, the term “complex” refers to an assemblage or aggregate of molecules (e.g., peptides, polypeptides, etc.) in direct and/or indirect contact with one another. In one aspect, “contact,” or more particularly, “direct contact” means two or more molecules are close enough so that attractive noncovalent interactions between the molecules, such as Van der Waal forces, hydrogen bonding, ionic and hydrophobic interactions, and the like, influence the interaction of the molecules. As used herein, the term “complex”, unless described as otherwise, refers to the assemblage of two or more molecules (e.g., peptides, polypeptides or a combination thereof).

As used herein, the term “non-luminescent” refers to an entity (e.g., peptide, polypeptide, complex, protein, etc.) that exhibits the characteristic of not emitting energy as light in the visible spectrum (e.g., in the presence or absence of a substrate). An entity may be referred to as non-luminescent if it does not exhibit detectable luminescence in a given assay. As used herein, the term “non-luminescent” is synonymous with the term “substantially non-luminescent.” An entity is “non-luminescent” if any light emission is sufficiently minimal so as not to interfere with the intended purpose for a particular assay.

As used herein, the terms “non-luminescent peptide” (NLpep) and “non-luminescent polypeptide” (NLpoly) refer to peptides and polypeptides (e.g., an internal tag, a complement sequence, etc.) that exhibit substantially no luminescence (e.g., in the presence or absence of a substrate), or an amount that is virtually undetectable (e.g., beneath the noise) under standard conditions (e.g., physiological conditions, assay conditions, etc.) and with typical instrumentation (e.g., luminometer, etc.). In some embodiments, such non-luminescent peptides and polypeptides assemble, according to the criteria described herein, to form a bioluminescent complex. As used herein, a “non-luminescent element” is a non-luminescent peptide or non-luminescent polypeptide. The term “bioluminescent complex” refers to the assembled complex of two or more non-luminescent peptides and/or non-luminescent polypeptides. The bioluminescent complex catalyzes or enables the conversion of a substrate for the bioluminescent complex into a high-energy reaction product; the reaction product subsequently emits light as it converts to a more stable form. When uncomplexed, two non-luminescent elements that form a bioluminescent complex may be referred to as a “non-luminescent pair.” If a bioluminescent complex is formed by three or more non-luminescent peptides and/or non-luminescent polypeptides, the uncomplexed constituents of the bioluminescent complex may be referred to as a “non-luminescent group.” As used herein, the term “non-luminescent complex” refers to a complex of two or more elements (e.g., peptides, polypeptides, etc.) that does not does not substantially catalyze the conversion of a substrate for the bioluminescent complex into a high-energy reaction product. In some embodiments, a “non-luminescent complex” requires an additional non-luminescent element (e.g., a third element) to form a luminescent complex.

As used herein, the term “interaction element” refers to a moiety that assists in bringing together a pair of non-luminescent elements (e.g., an internal tag and a complement sequence) or a non-luminescent group (e.g., an internal tag and a complement sequence) to form a bioluminescent complex. In a typical embodiment, a pair of interaction elements (a.k.a. “interaction pair”) is attached to a pair of non-luminescent elements (e.g., non-luminescent peptide/polypeptide pair), and the attractive interaction between the two interaction elements facilitates formation of the bioluminescent complex; although the present invention is not limited to such a mechanism, and an understanding of the mechanism is not required to practice the invention. Interaction elements may facilitate formation of the bioluminescent complex by any suitable mechanism (e.g., bringing non-luminescent pair/group into close proximity, placing a non-luminescent pair/group in proper conformation for interaction, reducing activation energy for complex formation, combinations thereof, etc.). An interaction element may be a protein, polypeptide, peptide, small molecule, cofactor, nucleic acid, lipid, carbohydrate, antibody, polymer, particle, etc. An interaction pair may be made of two of the same interaction elements (i.e. homopair) or two different interaction elements (i.e. heteropair). In the case of a heteropair, the interaction elements may be the same type of moiety (e.g., polypeptides) or may be two different types of moieties (e.g., polypeptide and small molecule). In some embodiments, in which complex formation by the interaction pair is studied, an interaction pair may be referred to as a “target pair” or a “pair of interest,” and the individual interaction elements are referred to as “target elements” (e.g., “target peptide,” “target polypeptide,” etc.) or “elements of interest” (e.g., “peptide of interest,” “polypeptide or interest,” etc.).

As used herein, the term “preexisting protein” refers to an amino acid sequence that was in physical existence prior to a certain event or date. A “peptide that is not a fragment of a preexisting protein” is a short amino acid chain that is not a fragment or sub-sequence of a protein (e.g., synthetic or naturally-occurring) that was in physical existence prior to the design and/or synthesis of the peptide.

As used herein, the term “fragment” refers to a peptide or polypeptide that results from dissection or “fragmentation” of a larger whole entity (e.g., protein, polypeptide, enzyme, etc.), or a peptide or polypeptide prepared to have the same sequence as such. Therefore, a fragment is a subsequence of the whole entity (e.g., protein, polypeptide, enzyme, etc.) from which it is made and/or designed. A peptide or polypeptide that is not a subsequence of a preexisting whole protein is not a fragment (e.g., not a fragment of a preexisting protein). A peptide or polypeptide that is “not a fragment of a preexisting bioluminescent protein” is an amino acid chain that is not a subsequence of a protein (e.g., natural of synthetic) that: (1) was in physical existence prior to design and/or synthesis of the peptide or polypeptide, and (2) exhibits substantial bioluminescent activity.

As used herein, the term “subsequence” refers to a peptide or polypeptide that has 100% sequence identify with another, larger peptide or polypeptide. The subsequence is a perfect sequence match for a portion of the larger amino acid chain.

As used herein, the term “sequence identity” refers to the degree two polymer sequences (e.g., peptide, polypeptide, nucleic acid, etc.) have the same sequential composition of monomer subunits. The term “sequence similarity” refers to the degree with which two polymer sequences (e.g., peptide, polypeptide, nucleic acid, etc.) have similar polymer sequences. For example, similar amino acids are those that share the same biophysical characteristics and can be grouped into the families, e.g., acidic (e.g., aspartate, glutamate), basic (e.g., lysine, arginine, histidine), non-polar (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan) and uncharged polar (e.g., glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine). The “percent sequence identity” (or “percent sequence similarity”) is calculated by: (1) comparing two optimally aligned sequences over a window of comparison (e.g., the length of the longer sequence, the length of the shorter sequence, a specified window), (2) determining the number of positions containing identical (or similar) monomers (e.g., same amino acids occurs in both sequences, similar amino acid occurs in both sequences) to yield the number of matched positions, (3) dividing the number of matched positions by the total number of positions in the comparison window (e.g., the length of the longer sequence, the length of the shorter sequence, a specified window), and (4) multiplying the result by 100 to yield the percent sequence identity or percent sequence similarity. For example, if peptides A and B are both 20 amino acids in length and have identical amino acids at all but 1 position, then peptide A and peptide B have 95% sequence identity. If the amino acids at the non-identical position shared the same biophysical characteristics (e.g., both were acidic), then peptide A and peptide B would have 100% sequence similarity. As another example, if peptide C is 20 amino acids in length and peptide D is 15 amino acids in length, and 14 out of 15 amino acids in peptide D are identical to those of a portion of peptide C, then peptides C and D have 70% sequence identity, but peptide D has 93.3% sequence identity to an optimal comparison window of peptide C. For the purpose of calculating “percent sequence identity” (or “percent sequence similarity”) herein, any gaps in aligned sequences are treated as mismatches at that position.

As used herein, the term “physiological conditions” encompasses any conditions compatible with living cells, e.g., predominantly aqueous conditions of a temperature, pH, salinity, chemical makeup, etc. that are compatible with living cells.

As used herein, the term “sample” is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum and the like. Sample may also refer to cell lysates or purified forms of the peptides and/or polypeptides described herein. Cell lysates may include cells that have been lysed with a lysing agent or lysates such as rabbit reticulocyte or wheat germ lysates. Sample may also include cell-free expression systems. Environmental samples include environmental material such as surface matter, soil, water, and industrial samples. Such examples are not however to be construed as limiting the sample types applicable to the present invention.

As used herein, unless otherwise specified, the terms “peptide” and “polypeptide” refer to polymer compounds of two or more amino acids joined through the main chain by peptide amide bonds (—C(O)NH—). The term “peptide” typically refers to short amino acid polymers (e.g., chains having fewer than 25 amino acids), whereas the term “polypeptide” typically refers to longer amino acid polymers (e.g., chains having more than 25 amino acids).

As used herein, the terms “fusion”, “fusion polypeptide”, and “fusion protein” refer to a chimeric protein containing a first protein or polypeptide of interest (e.g., target sequence, etc.) joined to a second different peptide, polypeptide, or protein (e.g., detectable sequence, isolatable sequence, tag, etc.). The term “internal fusion”, as used herein, refers to a fusion in which the second peptide, polypeptide, or protein is inserted at a position within the sequence of the first (e.g., not at the N- or C-terminus). The term “traditional fusion” refers to a fusion in which the first polypeptide or protein and the second peptide, polypeptide, or protein are fused end to end (e.g., C-terminus to N-terminus or N-terminus to C-terminus).

As used herein, the terms “coelenterazine” or “coelenterazine substrate” refer to naturally-occurring (“native”) coelenterazine. As used herein, the terms “a coelenterazine” or “a coelenterazine substrate” refers to native coelenterazine as well as synthetic, e.g., derivative or variant, and natural analogs thereof, including furimazine, coelenterazine-n, coelenterazine-f, coelenterazine-h, coelenterazine-hcp, coelenterazine-cp, coelenterazine-c, coelenterazine-e, coelenterazine-fcp, bis-deoxycoelenterazine (“coelenterazine-hh”), coelenterazine-i, coelenterazine-icp, coelenterazine-v, and 2-methyl coelenterazine, in addition to those disclosed in WO 2003/040100; U.S. application Ser. No. 12/056,073 (paragraph [0086]); and U.S. Pat. No. 8,669,103; the disclosures of which are incorporated by reference herein in their entireties.

As used herein, the term “low affinity” describes an intermolecular interaction between two entities (e.g., protein-protein) that is too weak to result in significant complex formation between the entities, except at concentrations substantially higher (e.g., 2-fold, 5-fold, 10-fold, 100-fold, 1000-fold, or more) than physiologic or assay conditions.

As used herein, the term “high affinity” describes an intermolecular interaction between two entities that is of sufficient strength to produce detectable complex formation under physiologic or assay conditions.

DETAILED DESCRIPTION

Tagging of proteins with reporters is commonly used to analyze protein function and behavior. In general, genetic fusions are generated using either the C- or N-terminus of the protein of interest. However, in certain cases, both termini are relevant to function of the protein of interest, and therefore cannot be modified without altering the physiological function of the protein. Embodiments described herein enable, for example, the analysis of protein-protein interactions without the need of modification of either the N- or C-terminus. Embodiments further enable detection and/or localization (e.g., cellular or subcellular localization) of a protein without the need of modification of either the N- or C-terminus. Various proteins undergo modifications that lead to changes in configuration; using an internal peptide/polypeptide tag that is accessible for structural complementation based on the configuration of the host protein enables the generation of biosensors using full length proteins. Therefore, provided herein are substantially non-luminescent peptide/polypeptide tags that are inserted internally within a protein of interest. Interaction of the internally-inserted tag with a complement polypeptide/peptide that is also substantially non-luminescent results in the formation a bioluminescent reporter complex.

Provided herein are compositions and methods for the assembly of a bioluminescent complex from an internal tag (e.g., peptide or polypeptide) of a protein or polypeptide and a structural complement thereof (e.g., free or in a fusion (e.g., internal or terminal)). In some embodiments, the internal tag and/or structural complement are not fragments of a preexisting protein (e.g., are not complementary subsequences of a known polypeptide sequence). In particular, bioluminescent activity is conferred upon a substantially non-luminescent internal tag of a protein/polypeptide via structural complementation with a substantially non-luminescent peptide structural complement sequence of the internal tag.

In some embodiments provided herein are substantially non-luminescent internal tags and structural complements thereof for use in detecting the presence of proteins/polypeptides of interest, and for monitoring molecular interactions (e.g., protein-protein, protein-DNA, protein-RNA interactions, protein-small molecule, etc.). Also provided herein are complementary panels of interchangeable internal tags and structural complement sequences (e.g., peptides and polypeptides) that have variable affinities and luminescence upon formation of the various bioluminescent complexes (e.g., a high-affinity/high-luminescence pair, a moderate-affinity/high-luminescence pair, a low-affinity/moderate-luminescence pair, etc.). Utilizing different combinations of internal tags and structural complements provides an adaptable system comprising various pairs ranging from lower to higher affinities, luminescence and other variable characteristics. This adaptability allows the detection/monitoring of proteins of interest and their molecular interactions to be fine-tuned to the specific molecule(s) of interest and expands the range of molecular interactions that can be monitored to include interactions with very high or low affinities. Further provided herein are methods by which internal tags, structural complements, and panels thereof are developed and tested.

In some embodiments, the affinity between the internal tag and the structural complement alone is insufficient to form the active (e.g., bioluminescent) complex and produce the resulting signal (e.g., bioluminescent signal). However, if the structural complement is fused, tethered, attached, etc., to an interaction moiety (e.g., peptide, protein, nucleic acid, small molecule, etc.) that interacts with the internally tagged polypeptide, then that interaction (e.g., complex formation between the polypeptide of interest and the interaction moiety) facilitates formation of the bioluminescent complex. In such embodiments, the signal from the bioluminescent complex in the presence of a substrate serves as an indication for the formation of the complex of the polypeptide of interest and the integration moiety (a.k.a., interaction complex). If an interaction complex is formed, then a bioluminescent complex is formed, and a bioluminescent signal is generated, which can then be detected/measured/monitored (e.g., in the presence of substrate). If an interaction complex fails to form (e.g., due to unfavorable conditions, due to unstable interaction between the interaction elements, due to incompatible interaction elements, etc.), then a stable bioluminescent complex does not form, and a bioluminescent signal is not produced.

In certain embodiments, an internally tagged polypeptide and a second moiety that interacts (e.g., forms a complex) therewith are known as an interaction pair. In some embodiments, an interaction pair comprises two molecules of interest (e.g., proteins of interest). In some embodiments, at least one member of an interaction pair is internally tagged. In some embodiments, both members of an interaction pair are internally tagged (e.g., with structurally complementary internal tags). In some embodiments, one member of an interaction pair is internally tagged and the other is terminally tagged. For example, assays are performed to detect the interaction of a protein of interest and a second molecule of interest (e.g., peptide, protein, nucleic acid, small molecule, etc.) by inserting an internal tag into the protein of interest and tethering (e.g., internal tag, terminal tag, etc.) the molecule of interest to a structural complement of the internal tag. If the protein of interest and the molecule of interest interact (e.g., transiently interact, stably interact, etc.), the internal tag and structural complement are brought into close proximity in a suitable conformation to form an active complex (e.g., a bioluminescent complex) signal is produced/detected (e.g., in the presence of substrate). In the absence of an interaction between the protein of interest and the molecule of interest, the internal tag and structural complement do not interact in a stable enough manner, and a signal is not produced or only weakly produced. Such embodiments find use to study the effect of inhibitors on complex formation, the effect of mutations on complex formation, the effect of conditions (e.g., temperature, pH, etc.) on complex formation, the interaction of a small molecule (e.g., potential therapeutic) with a target molecule, etc.

In some embodiments, an internally-tagged protein of interest is monitored (e.g., detected, localized, etc.) by the formation of an active (e.g., bioluminescent) complex with a free structural complement. In such embodiments, an internal tag and structural complement are selected with sufficiently high affinity for each other such that detectable complex forms when both an internally tagged protein and the free structural complement are present.

Different internal tag and structural complement pairs may require different strength, duration and/or stability of the interaction complex to result in active (e.g., bioluminescent) complex formation. In some embodiments, a stable interaction complex is required to produce a detectable (e.g., bioluminescent) signal. In other embodiments, even a weak or transient interaction complex results in active (e.g., bioluminescent) complex formation. In some embodiments, the strength of an interaction complex is directly proportional to the strength of the resulting (e.g., bioluminescent) signal. Some internal tag and structural complement pairs produce a detectable signal when combined with an interaction pair (e.g., internally-tagged protein of interest and interaction partner) with a high millimolar dissociation constant (e.g., K_(d)>100 mM). Other internal tag and structural complement pairs require an interaction pair with a low millimolar (e.g., K_(d)<100 mM), micromolar (e.g., K_(d)<1 mM), nanomolar (e.g., K_(d)<1 μM), or even picomolar (e.g., K_(d)<1 nM) dissociation constant in order to produce a bioluminescent complex with a detectable signal. Still other internal tag and structural complement pairs form an active complex in the absence of any interaction pair.

In some embodiments, one or both of the internal tag and structural complement are not fragments of a pre-existing protein. In some embodiments, one or both of the internal tag and structural complement are not fragments of a pre-existing bioluminescent protein. In some embodiments, neither the internal tag nor the structural complement is a fragment of a pre-existing protein. In some embodiments, neither the internal tag nor the structural complement is a fragment of a pre-existing bioluminescent protein.

In some embodiments, both the internal tag and its structural complement are substantially inactive (e.g., non-luminescent) in isolation. In certain embodiments, when placed in suitable conditions (e.g., physiological conditions), the substantially non-luminescent internal tag and its substantially non-luminescent structural complement interact to form a bioluminescent complex and produce a bioluminescent signal in the presence of substrate. In some embodiments, an internal tag and its structural complement produce a low level of activity (e.g., bioluminescence) in each other's presence, but undergo a significant increase in detectable activity (e.g., bioluminescence) under a particular set of conditions.

In some embodiments, compositions and methods described herein comprise one or more interaction elements. In a typical embodiment, an interaction element is a moiety (e.g., peptide, polypeptide, protein, small molecule, nucleic acid, lipid, carbohydrate, etc.) that is attached to a structural complement of the internally tag, and associates or forms a complex with the internally-tagged protein to facilitate assembly of the complex of the internal tag and its structural complement.

In some embodiments, an interaction pair comprises the internally-tagged protein or polypeptide and any other suitable chemical moiety that interacts with the internally-tagged protein or polypeptide to facilitate assembly of the active complex of the internal tag and its structural complement. An interaction pair may consist of, for example: an internally tagged protein and: a nucleic acid, a polypeptide, a protein, a ligand, a small molecule, an antibody, a lipid, etc. Any molecular entity capable of interacting with the internally tagger protein or polypeptide may find use in some embodiments herein.

In some embodiments, compositions and methods herein provide useful assays (e.g., in vitro, in vivo, in situ, whole animal, etc.) for studying the interactions between a pair of target molecules (e.g., the internally-tagged protein and a (potential) interaction partner).

In some embodiments, the presence of a ligand, substrate, co-factor, etc., is necessary to induce the interaction between the internally-tagged protein and its interaction partner, in order to facilitate formation of the complex (e.g., bioluminescent complex) between the internal tag and the structural complement linked to the interaction partner. In some embodiments, detecting a signal from the bioluminescent complex indicates the presence of the ligand, substrate, co-factor, etc.

In some embodiments, an internal tag and its structural complement are present in a single amino acid chain (e.g., N-(amino acid sequence 1)-(internal tag)-(amino acid sequence 2)-(structural complement)-C, etc.). In some embodiments, folding of the protein of interest results in formation of the active complex (e.g., bioluminescent complex).

In some embodiments, an internally-tagged protein and fusion of an interaction peptide or polypeptide and a structural complement of the internal tag are expressed within the same cells. In such embodiments, an internally-tagged protein and fusion of an interaction peptide or polypeptide and a structural complement of the internal tag are purified and/or isolated from the cells, or the interaction is assayed within the cells. In some embodiments, an internally-tagged protein and fusion of an interaction peptide or polypeptide and a structural complement of the internal tag are stably expressed. In some embodiments, an internally-tagged protein and fusion of an interaction peptide or polypeptide and a structural complement of the internal tag are transiently expressed. In other embodiments, an internally-tagged protein and fusion of an interaction peptide or polypeptide and a structural complement of the internal tag are expressed in separate cells and combined (e.g., following purification and/or isolation) for signal detection. In some embodiments, an internally-tagged protein and fusion of an interaction peptide or polypeptide and a structural complement of the internal tag are expressed in cell lysate (e.g., rabbit reticulocyte lysate) or in a cell-free system.

In certain embodiments, nucleic acids, DNA, RNA, vectors, etc. are provided that encode the peptides, polypeptides, fusion polypeptides, fusion proteins, etc., described herein. Such nucleic acids and vectors may be used for expression, transformation, transfection, injection, etc.

In some embodiments, an internal tag is attached (e.g., on its N-terminus, on its C-terminus, at both ends) to polypeptide sequence by a linker. In some embodiments, structural complement is attached (e.g., on its N-terminus, on its C-terminus, at both ends) to a molecule of interest (e.g., protein of interest) by a linker. In some embodiments, a linker provides a connection and allows a desired amount of space/distance between the elements. In certain embodiments, a linker provides appropriate attachment chemistry between the linked elements. In some embodiments, a linker is any suitable chemical moiety capable of linking, connecting, or tethering two elements (e.g., peptides, polypeptides, small molecules, etc.). In some embodiments, a linker is a polymer of one or more repeating or non-repeating monomer units (e.g., nucleic acid, amino acid, carbon-containing polymer, carbon chain, etc.). A wide variety of linkers may be used. In some embodiments, the linker is a single covalent bond. In some embodiments, the linker comprises a linear or branched, cyclic or heterocyclic, saturated or unsaturated, structure having 1-20 nonhydrogen atoms (e.g., C, N, P, O and S) and is composed of any combination of alkyl, ether, thioether, imine, carboxylic, amine, ester, carboxamide, sulfonamide, hydrazide bonds and aromatic or heteroaromatic bonds. In some embodiments, linkers are longer than 20 nonhydrogen atoms (e.g. 21 non-hydrogen atoms, 25 non-hydrogen atoms, 30 non-hydrogen atoms, 40 non-hydrogen atoms, 50 non-hydrogen atoms, 100 non-hydrogen atoms, etc.) In some embodiments, the linker comprises 1-50 non-hydrogen atoms (in addition to hydrogen atoms) selected from the group of C, N, P, O and S (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 non-hydrogen atoms).

The present invention is not limited by the types of linkers available. The signal and interaction elements are linked, either directly (e.g. linker consists of a single covalent bond) or linked via a suitable linker. The present invention is not limited to any particular linker group. A variety of linker groups are contemplated, and suitable linkers could comprise, but are not limited to, alkyl groups, methylene carbon chains, ether, polyether, alkyl amide linker, a peptide linker, a modified peptide linker, a Poly(ethylene glycol) (PEG) linker, a streptavidin-biotin or avidin-biotin linker, polyaminoacids (e.g. polylysine), functionalised PEG, polysaccharides, glycosaminoglycans, dendritic polymers (WO93/06868 and by Tomalia et al. in Angew. Chem. Int. Ed. Engl. 29:138-175 (1990), herein incorporated by reference in their entireties), PEG-chelant polymers (W94/08629, WO94/09056 and WO96/26754, herein incorporated by reference in their entireties), oligonucleotide linker, phospholipid derivatives, alkenyl chains, alkynyl chains, disulfide, or a combination thereof.

In some embodiments, the linker is cleavable (e.g., enzymatically (e.g., TEV protease site), chemically, photoinduced, etc.).

In some embodiments, substantially non-luminescent internal tags are directly linked to peptide and/or polypeptide sequences. In some embodiments, two or more internal tags reside at a location internal to a polypeptide of interest. In some embodiments, one or more internal tags serve a linker function, rather than a reporter function.

In some embodiments, substantially non-luminescent internal tags and structural complements thereof are provided with less than 100% sequence identity and/or similarity to any portion of an existing luciferase (e.g., a firefly luciferase, a Renilla luciferase, an Oplophorus luciferase, enhanced Oplophorus luciferases as described in U.S. Pat. No. 8,557,970; U.S. Pat. App. 2014/0120548; U.S. Pat. No. 8,669,103; U.S. patent application Ser. No. 14/160,278; and U.S. patent application Ser. No. 14/160,282, herein incorporated by reference in their entireties). Certain embodiments of the present invention involve the formation of bioluminescent complexes of substantially non-luminescent internal tags and substantially non-luminescent structural complements with less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity with all or a portion (e.g., >5, >8, >10, >12, >15, >20, <15, <18, <20, <22, <25, <30, <40, and ranges defined thereby) of SEQ ID NO: 2157 (e.g., complete NANOLUC sequence). In some embodiments, substantially non-luminescent internal tags and substantially non-luminescent structural complements are provided with less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence similarity with a portion (e.g., >5, >8, >10, >12, >15, >20, <15, <18, <20, <22, <25, <30, <40, and ranges defined thereby) of SEQ ID NO: 2157 (e.g., peptides and polypeptides that interact to form bioluminescent complexes). In some embodiments, substantially non-luminescent internal tags and substantially non-luminescent structural complements are provided that have less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity and/or similarity with about a 25 amino acid or less portion of SEQ ID NO: 2157, wherein such peptides form a bioluminescent complex when combined under appropriate conditions (e.g., stabilized by an interaction pair) with a polypeptide having less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity and/or similarity with another portion SEQ ID NO: 2157. Similarly, substantially non-luminescent internal tags and substantially non-luminescent structural complements are provided that have less than 100%, but more than 40% (e.g., >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity or similarity with a portion of SEQ ID NO: 2157, wherein such substantially non-luminescent internal tags and substantially non-luminescent structural complements form a bioluminescent complex when combined under appropriate conditions (e.g., stabilized by an interaction pair) with a peptide having less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity and/or similarity with another portion SEQ ID NO: 2157. In some embodiments, substantially non-luminescent internal tags and substantially non-luminescent structural complements with less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity or similarity with SEQ ID NO: 2 are provided. In some embodiments, substantially non-luminescent internal tags and substantially non-luminescent structural complements with less than 100%, but more than 30% (e.g., >30%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >90%, >95%, >98%, >99%) sequence identity or similarity with SEQ ID NO: 440 are provided.

In some embodiments, internal tags and/or structural complements that find use in embodiments of the present invention include peptides with one or more amino acid substitutions, deletions, or additions from GVTGWRLCKRILA (SEQ ID NO: 2). In some embodiments, the provided herein are internal tags and/or structural complements comprising an amino acid sequence of Table 1, and/or nucleic acids comprising the nucleic acid sequences of Table 1 (which code for the peptide sequences of Table 1).

TABLE 1 Exemplary internal tag and/or structural complement peptide sequences SEQ ID POLY NO. PEPTIDE NO. MER SEQUENCE 3 NLpep2 (w/ Met) N.A. ATGGACGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCG 4 NLpep2 (w/ Met) A.A. MDVTGWRLCERILA 5 NLpep3 (w/ Met) N.A. ATGGGAGTGACCGCCTGGCGGCTGTGCGAACGCATTCTGGCG 6 NLpep3 (w/ Met) A.A. MGVTAWRLCERILA 7 NLpep4 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTCTGGCG 8 NLpep4 (w/ Met) A.A. MGVTGWRLCKRILA 9 NLpep5 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCGAACGCATTAGCGCG 10 NLpep5 (w/ Met) A.A. MGVTGWRLCERISA 11 NLpep6 (w/ Met) N.A. ATGGACGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 12 NLpep6 (w/ Met) A.A. MDVTGWRLCKRISA 13 NLpep7 (w/ Met) N.A. ATGGACGTGACCGGCTGGCGGCTGTGCAAGCGCATTCTGGCG 14 NLpep7 (w/ Met) A.A. MDVTGWRLCKRILA 15 NLpep8 (w/ Met) N.A. ATGGACGTGACCGGCTGGCGGCTGTGCGAACGCATTAGCGCG 16 NLpep8 (w/ Met) A.A. MDVTGWRLCERISA 17 NLpep9 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 18 NLpep9 (w/ Met) A.A. MGVTGWRLCKRISA 19 NLpep10 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGAACGAACGCATTCTGGCG 20 NLpep10 (w/ Met) A.A. MGVTGWRLNERILA 21 NLpep11 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGCAGGAACGCATTCTGGCG 22 NLpep11 (w/ Met) A.A. MGVTGWRLQERILA 23 NLpep12 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGAAGAAGCGCCGGAGCCGG 24 NLpep12 (w/ Met) A.A. MGVTGWRLKKRRSR 25 NLpep13 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 26 NLpep13 (w/ Met) A.A. MNVTGWRLCKRISA 27 NLpep14 (w/ Met) N.A. ATGAGCGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 28 NLpep14 (w/ Met) A.A. MSVTGWRLCKRISA 29 NLpep15 (w/ Met) N.A. ATGGAGGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 30 NLpep15 (w/ Met) A.A. MEVTGWRLCKRISA 31 NLpep16 (w/ Met) N.A. ATGGGCGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 32 NLpep16 (w/ Met) A.A. MHVTGWRLCKRISA 33 NLpep17 (w/ Met) N.A. ATGGGACACACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 34 NLpep17 (w/ Met) A.A. MGITGWRLCKRISA 35 NLpep18 (w/ Met) N.A. ATGGGAGCCACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 36 NLpep18 (w/ Met) A.A. MGATGWRLCKRISA 37 NLpep19 (w/ Met) N.A. ATGGGAAAGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 38 NLpep19 (w/ Met) A.A. MGKTGWRLCKRISA 39 NLpep20 (w/ Met) N.A. ATGGGACAGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 40 NLpep20 (w/ Met) A.A. MGQTGWRLCKRISA 41 NLpep21 (w/ Met) N.A. ATGGGAAGCACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 42 NLpep21 (w/ Met) A.A. MGSTGWRLCKRISA 43 NLpep22 (w/ Met) N.A. ATGGGAGTGGTGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 44 NLpep22 (w/ Met) A.A. MGVVGWRLCKRISA 45 NLpep23 (w/ Met) N.A. ATGGGAGTGAAGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 46 NLpep23 (w/ Met) A.A. MGVKGWRLCKRISA 47 NLpep24 (w/ Met) N.A. ATGGGAGTGCAGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 48 NLpep24 (w/ Met) A.A. MGVQGWRLCKRISA 49 NLpep25 (w/ Met) N.A. ATGGGAGTGACCGGCACCCGGCTGTGCAAGCGCATTAGCGCG 50 NLpep25 (w/ Met) A.A. MGVTGTRLCKRISA 51 NLpep26 (w/ Met) N.A. ATGGGAGTGACCGGCAAGCGGCTGTGCAAGCGCATTAGCGCG 52 NLpep26 (w/ Met) A.A. MGVTGKRLCKRISA 53 NLpep27 (w/ Met) N.A. ATGGGAGTGACCGGCGTGCGGCTGTGCAAGCGCATTAGCGCG 54 NLpep27 (w/ Met) A.A. MGVTGVRLCKRISA 55 NLpep28 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCACTGCAAGCGCATTAGCGCG 56 NLpep28 (w/ Met) A.A. MGVTGWRICKRISA 57 NLpep29 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGGTGTGCAAGCGCATTAGCGCG 58 NLpep29 (w/ Met) A.A. MGVTGWRVCKRISA 59 NLpep30 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGACCTGCAAGCGCATTAGCGCG 60 NLpep30 (w/ Met) A.A. MGVTGWRTCKRISA 61 NLpep31 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGTACTGCAAGCGCATTAGCGCG 62 NLpep31 (w/ Met) A.A. MGVTGWRYCKRISA 63 NLpep32 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGAAGTGCAAGCGCATTAGCGCG 64 NLpep32 (w/ Met) A.A. MGVTGWRKCKRISA 65 NLpep33 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGAACAAGCGCATTAGCGCG 66 NLpep33 (w/ Met) A.A. MGVTGWRLNKRISA 67 NLpep34 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGACCAAGCGCATTAGCGCG 68 NLpep34 (w/ Met) A.A. MGVTGWRLTKRISA 69 NLpep35 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGAAGATTAGCGCG 70 NLpep35 (w/ Met) A.A. MGVTGWRLCKKISA 71 NLpep36 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGAACATTAGCGCG 72 NLpep36 (w/ Met) A.A. MGVTGWRLCKNISA 73 NLpep37 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCGTGAGCGCG 74 NLpep37 (w/ Met) A.A. MGVTGWRLCKRVSA 75 NLpep38 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCCAGAGCGCG 76 NLpep38 (w/ Met) A.A. MGVTGWRLCKRQSA 77 NLpep39 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCGAGAGCGCG 78 NLpep39 (w/ Met) A.A. MGVTGWRLCKRESA 79 NLpep40 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCCGGAGCGCG 80 NLpep40 (w/ Met) A.A. MGVTGWRLCKRRSA 81 NLpep41 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCTTCAGCGCG 82 NLpep41 (w/ Met) A.A. MGVTGWRLCKRFSA 83 NLpep42 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCAAC 84 NLpep42 (w/ Met) A.A. MGVTGWRLCKRISN 85 NLpep43 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCACC 86 NLpep43 (w/ Met) A.A. MGVTGWRLCKRIST 87 NLpep44 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCCGG 88 NLpep44 (w/ Met) A.A. MGVTGWRLCKRISR 89 NLpep45 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCCTG 90 NLpep45 (w/ Met) A.A. MGVTGWRLCKRISL 91 NLpep46 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGAG 92 NLpep46 (w/ Met) A.A. MGVTGWRLCKRISE 93 NLpep47 (w/ Met) N.A. ATGGGAGTGACCGGCTTCCGGCTGTGCAAGCGCATTAGCGCG 94 NLpep47 (w/ Met) A.A. MGVTGFRLCKRISA 95 NLpep48 (w/ Met) N.A. ATGGGAGTGACCGGCTACCGGCTGTGCAAGCGCATTAGCGCG 96 NLpep48 (w/ Met) A.A. MGVTGYRLCKRISA 97 NLpep49(w/ Met) N.A. ATGGGAGTGACCGGCGAGCGGCTGTGCAAGCGCATTAGCGCG 98 NLpep49(w/ Met) A.A. MGVTGERLCKRISA 99 NLpep50 (w/ Met) N.A. ATGCAGGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 100 NLpep50 (w/ Met) A.A. MQVTGWRLCKRISA 101 NLpep51 (w/ Met) N.A. ATGACCGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 102 NLpep51 (w/ Met) A.A. MTVTGWRLCKRISA 103 NLpep52 (w/ Met) N.A. ATGGGAGTGGAGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 104 NLpep52 (w/ Met) A.A. MGVEGWRLCKRISA 105 NLpep53 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 106 NLpep53 (w/ Met) A.A. MGVTGWRLFKRISA 107 NLpep54 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTACAAGCGCATTAGCGCG 108 NLpep54 (w/ Met) A.A. MGVTGWRLYKRISA 109 NLpep55 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGAGCAAGCGCATTAGCGCG 110 NLpep55 (w/ Met) A.A. MGVTGWRLSKRISA 111 NLpep56 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGGGCAAGCGCATTAGCGCG 112 NLpep56 (w/ Met) A.A. MGVTGWRLHKRISA 113 NLpep57 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGATGAAGCGCATTAGCGCG 114 NLpep57 (w/ Met) A.A. MGVTGWRLMKRISA 115 NLpep58 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGGCCAAGCGCATTAGCGCG 116 NLpep58 (w/ Met) A.A. MGVTGWRLAKRISA 117 NLpep59 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGCAGAAGCGCATTAGCGCG 118 NLpep59 (w/ Met) A.A. MGVTGWRLQKRISA 119 NLpep60 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGCTGAAGCGCATTAGCGCG 120 NLpep60 (w/ Met) A.A. MGVTGWRLLKRISA 121 NLpep61 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGAAGAAGCGCATTAGCGCG 122 NLpep61 (w/ Met) A.A. MGVTGWRLKKRISA 123 NLpep62 (w/ Met) N.A. ATGAACCACACCGGCTGGCGGCTGAACAAGAAGGTGAGCAAC 124 NLpep62 (w/ Met) A.A. MNITGWRLNKKVSN 125 NLpep63 (w/ Met) N.A. ATGAACCACACCGGCTACCGGCTGAACAAGAAGGTGAGCAAC 126 NLpep63 (w/ Met) A.A. MNITGYRLNKKVSN 127 NLpep64 (w/ Met) N.A. ATGTGCGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 128 NLpep64 (w/ Met) A.A. MCVTGWRLFKRISA 129 NLpep65 (w/ Met) N.A. ATGCCCGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 130 NLpep65 (w/ Met) A.A. MPVTGWRLFKRISA 131 NLpep66 (w/ Met) N.A. ATGAACCACACCGGCTACCGGCTGTTCAAGAAGGTGAGCAAC 132 NLpep66 (w/ Met) A.A. MNITGYRLFKKVSN 133 NLpep67 (w/ Met) N.A. ATGAACGTGACCGGCTACCGGCTGTTCAAGAAGGTGAGCAAC 134 NLpep67 (w/ Met) A.A. MNVTGYRLFKKVSN 135 NLpep68 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCAAGAAGGTGAGCAAC 136 NLpep68 (w/ Met) A.A. MNVTGWRLFKKVSN 137 NLpep69 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 138 NLpep69 (w/ Met) A.A. MNVTGWRLFKKISN 139 NLpep70 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCAAC 140 NLpep70 (w/ Met) A.A. MNVTGWRLFKRISN 141 NLpep71 (w/ Met) N.A. ATGGGAGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCAAC 142 NLpep71 (w/ Met) A.A. MGVTGWRLFKRISN 143 NLpep72 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCGAACGCATTAGCAAC 144 NLpep72 (w/ Met) A.A. MNVTGWRLFERISN 145 NLpep73 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCAAGCGCATTCTGAAC 146 NLpep73 (w/ Met) A.A. MNVTGWRLFKRILN 147 NLpep74 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 148 NLpep74 (w/ Met) A.A. MNVTGWRLFKRISA 149 NLpep75 (w/ Met) N.A. ATGAACGTGACCGGCTGGCGGCTGTTCGAAAAGATTAGCAAC 150 NLpep75 (w/ Met) A.A. MNVTGWRLFEKISN 151 NLpep76 (w/ Met) N.A. ATGAACGTGAGCGGCTGGCGGCTGTTCGAAAAGATTAGCAAC 152 NLpep76 (w/ Met) A.A. MNVSGWRLFEKISN 153 NLpep77 (w/ Met) N.A. ATG-GTGACCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 154 NLpep77 (w/ Met) A.A. M-VTGWRLFKKISN 155 NLpep78 (w/ Met) N.A. ATGAACGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 156 NLpep78 (w/ Met) A.A. MNVSGWRLFKKISN 157 NLpep79 (w/ Met) N.A. ATGAACGTGACCGGCTACCGGCTGTTCAAGAAGATTAGCAAC 158 NLpep79 (w/ Met) A.A. MNVTGYRLFKKISN 159 NLpep80(w/ Met) N.A. ATGGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 160 NLpep80(w/ Met) A.A. MVSGWRLFKKISN 161 NLpep81 (w/ Met) N.A. ATGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 440 NLpep81 (w/ Met) A.A. MSGWRLFKKISN 163 NLpep82 (w/ Met) N.A. ATGGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 164 NLpep82 (w/ Met) A.A. MGWRLFKKISN 165 NLpep83 (w/ Met) N.A. ATGAACGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGC 166 NLpep83 (w/ Met) A.A. MNVSGWRLFKKIS 167 NLpep84 (w/ Met) N.A. ATGAACGTGAGCGGCTGGCGGCTGTTCAAGAAGATT 168 NLpep84 (w/ Met) A.A. MNVSGWRLFKKI 169 NLpep85 (w/ Met) N.A. ATGAACGTGAGCGGCTGGCGGCTGTTCAAGAAG 170 NLpep85 (w/ Met) A.A. MNVSGWRLFKK 171 NLpep86 (w/ Met) N.A. ATGGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGC 172 NLpep86 (w/ Met) A.A. MVSGWRLFKKIS 173 NLpep87 (w/ Met) N.A. ATGAGCGGCTGGCGGCTGTTCAAGAAGATT 174 NLpep87 (w/ Met) A.A. MSGWRLFKKI 175 NLpep88 (w/ Met) N.A. ATGAACGTGAGCGGCTGGGGCCTGTTCAAGAAGATTAGCAAC 176 NLpep88 (w/ Met) A.A. MNVSGWGLFKKISN 177 NLpep89 (w/ Met) N.A. ATGCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 178 NLpep89 (w/ Met) A.A. MPVSGWRLFKKISN 179 NLpep90 (w/ Met) N.A. ATGAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 180 NLpep90 (w/ Met) A.A. MNPVSGWRLFKKISN 181 NLpep91 (w/ Met) N.A. ATGATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCA AC 182 NLpep91 (w/ Met) A.A. MINPVSGWRLFKKISN 183 NLpep92 (w/ Met) N.A. ATGACCATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTA GCAAC 184 NLpep92 (w/ Met) A.A. MTINPVSGWRLFKKISN 185 NLpep93 (w/ Met) N.A. ATGGTGACCATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAG ATTAGCAAC 186 NLpep93 (w/ Met) A.A. MVTINPVSGWRLFKKISN 187 NLpep94 (w/ Met) N.A. ATGCGGGTGACCATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGA AGATTAGCAAC 188 NLpep94 (w/ Met) A.A. MRVTINPVSGWRLFKKISN 189 NLpep95 (w/ Met) N.A. ATGAGCGGCTGGCGGCTGCTGAAGAAGATT 190 NLpep95 (w/ Met) A.A. MSGWRLLKKI 191 NLpep96 (w/ Met) N.A. ATGACCGGCTACCGGCTGCTGAAGAAGATT 192 NLpep96 (w/ Met) A.A. MTGYRLLKKI 193 NLpep97(w/ Met) N.A. ATGAGCGGCTGGCGGCTGTTCAAGAAG 194 NLpep97 (w/ Met) A.A. MSGWRLFKK 195 NLpep98 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCAAGAAGATTAGC 196 NLpep98 (w/ Met) A.A. MVTGYRLFKKIS 197 NLpep99 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGAAGATTAGC 198 NLpep99 (w/ Met) A.A. MVTGYRLFEKIS 199 NLpep100 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGCAGATTAGC 200 NLpep100 (w/ Met) A.A. MVTGYRLFEQIS 201 NLpep101 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGAAGGAGAGC 202 NLpep101 (w/ Met) A.A. MVTGYRLFEKES 203 NLpep102 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGCAGGAGAGC 204 NLpep102 (w/ Met) A.A. MVTGYRLFEQES 205 NLpep103 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGCAGGAGCTG 206 NLpep103 (w/ Met) A.A. MVTGYRLFEQEL 207 NLpep104 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGAAGATTAGC 208 NLpep104 (w/ Met) A.A. MVEGYRLFEKIS 209 NLpep105 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGCAGATTAGC 210 NLpep105 (w/ Met) A.A. MVEGYRLFEQIS 211 NLpep106 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGAAGGAGAGC 212 NLpep106 (w/ Met) A.A. MVEGYRLFEKES 213 NLpep107 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGCAGGAGAGC 214 NLpep107 (w/ Met) A.A. MVEGYRLFEQES 215 NLpep108 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGCAGGAGCTG 216 NLpep108 (w/ Met) A.A. MVEGYRLFEQEL 217 NLpep109 (w/ Met) N.A. ATGATTAGCGGCTGGCGGCTGATGAAGAACATTAGC 218 NLpep109 (w/ Met) A.A. MISGWRLMKNIS 219 NLpep110 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCAAGAAGATTAGC 220 NLpep110 (w/ Met) A.A. MVEGYRLFKKIS 221 NLpep2 (w/o Met) N.A. GACGTGACCGGCTGGCGGCTGTGCGAACGCATTCTGGCG 222 NLpep2 (w/o Met) A.A. DVTGWRLCERILA 223 NLpep3 (w/o Met) N.A. GGAGTGACCGCCTGGCGGCTGTGCGAACGCATTCTGGCG 224 NLpep3 (w/o Met) A.A. GVTAWRLCERILA 225 NLpep4 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTCTGGCG 226 NLpep4 (w/o Met) A.A. GVTGWRLCKRILA 227 NLpep5 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCGAACGCATTAGCGCG 228 NLpep5 (w/o Met) A.A. GVTGWRLCERISA 229 NLpep6 (w/o Met) N.A. GACGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 230 NLpep6 (w/o Met) A.A. DVTGWRLCKRISA 231 NLpep7 (w/o Met) N.A. GACGTGACCGGCTGGCGGCTGTGCAAGCGCATTCTGGCG 232 NLpep7 (w/o Met) A.A. DVTGWRLCKRILA 233 NLpep8 (w/o Met) N.A. GACGTGACCGGCTGGCGGCTGTGCGAACGCATTAGCGCG 234 NLpep8 (w/o Met) A.A. DVTGWRLCERISA 235 NLpep9 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 236 NLpep9 (w/o Met) A.A. GVTGWRLCKRISA 237 NLpep10 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGAACGAACGCATTCTGGCG 238 NLpep10 (w/o Met) A.A. GVTGWRLNERILA 239 NLpep11 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGCAGGAACGCATTCTGGCG 240 NLpep11 (w/o Met) A.A. GVTGWRLQERILA 241 NLpep12 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGAAGAAGCGCCGGAGCCGG 242 NLpep12 (w/o Met) A.A. GVTGWRLKKRRSR 243 NLpep13 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 244 NLpep13 (w/o Met) A.A. NVTGWRLCKRISA 245 NLpep14 (w/o Met) N.A. AGCGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 246 NLpep14 (w/o Met) A.A. SVTGWRLCKRISA 247 NLpep15 (w/o Met) N.A. GAGGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 248 NLpep15 (w/o Met) A.A. EVTGWRLCKRISA 249 NLpep16 (w/o Met) N.A. GGCGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 250 NLpep16 (w/o Met) A.A. HVTGWRLCKRISA 251 NLpep17 (w/o Met) N.A. GGACACACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 252 NLpep17 (w/o Met) A.A. GITGWRLCKRISA 253 NLpep18 (w/o Met) N.A. GGAGCCACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 254 NLpep18 (w/o Met) A.A. GATGWRLCKRISA 255 NLpep19 (w/o Met) N.A. GGAAAGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 256 NLpep19 (w/o Met) A.A. GKTGWRLCKRISA 257 NLpep20 (w/o Met) N.A. GGACAGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 258 NLpep20 (w/o Met) A.A. GQTGWRLCKRISA 259 NLpep21 (w/o Met) N.A. GGAAGCACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 260 NLpep21 (w/o Met) A.A. GSTGWRLCKRISA 261 NLpep22 (w/o Met) N.A. GGAGTGGTGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 262 NLpep22 (w/o Met) A.A. GVVGWRLCKRISA 263 NLpep23 (w/o Met) N.A. GGAGTGAAGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 264 NLpep23 (w/o Met) A.A. GVKGWRLCKRISA 265 NLpep24 (w/o Met) N.A. GGAGTGCAGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 266 NLpep24 (w/o Met) A.A. GVQGWRLCKRISA 267 NLpep25 (w/o Met) N.A. GGAGTGACCGGCACCCGGCTGTGCAAGCGCATTAGCGCG 268 NLpep25 (w/o Met) A.A. GVTGTRLCKRISA 269 NLpep26 (w/o Met) N.A. GGAGTGACCGGCAAGCGGCTGTGCAAGCGCATTAGCGCG 270 NLpep26 (w/o Met) A.A. GVTGKRLCKRISA 271 NLpep27 (w/o Met) N.A. GGAGTGACCGGCGTGCGGCTGTGCAAGCGCATTAGCGCG 272 NLpep27 (w/o Met) A.A. GVTGVRLCKRISA 273 NLpep28 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCACTGCAAGCGCATTAGCGCG 274 NLpep28 (w/o Met) A.A. GVTGWRICKRISA 275 NLpep29 (w/o Met) N.A. GGAGTGACCGGCTGGCGGGTGTGCAAGCGCATTAGCGCG 276 NLpep29 (w/o Met) A.A. GVTGWRVCKRISA 277 NLpep30 (w/o Met) N.A. GGAGTGACCGGCTGGCGGACCTGCAAGCGCATTAGCGCG 278 NLpep30 (w/o Met) A.A. GVTGWRTCKRISA 279 NLpep31 (w/o Met) N.A. GGAGTGACCGGCTGGCGGTACTGCAAGCGCATTAGCGCG 280 NLpep31 (w/o Met) A.A. GVTGWRYCKRISA 281 NLpep32 (w/o Met) N.A. GGAGTGACCGGCTGGCGGAAGTGCAAGCGCATTAGCGCG 282 NLpep32 (w/o Met) A.A. GVTGWRKCKRISA 283 NLpep33 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGAACAAGCGCATTAGCGCG 284 NLpep33 (w/o Met) A.A. GVTGWRLNKRISA 285 NLpep34 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGACCAAGCGCATTAGCGCG 286 NLpep34 (w/o Met) A.A. GVTGWRLTKRISA 287 NLpep35 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGAAGATTAGCGCG 288 NLpep35 (w/o Met) A.A. GVTGWRLCKKISA 289 NLpep36 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGAACATTAGCGCG 290 NLpep36 (w/o Met) A.A. GVTGWRLCKNISA 291 NLpep37 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCGTGAGCGCG 292 NLpep37 (w/o Met) A.A. GVTGWRLCKRVSA 293 NLpep38 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCCAGAGCGCG 294 NLpep38 (w/o Met) A.A. GVTGWRLCKRQSA 295 NLpep39 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCGAGAGCGCG 296 NLpep39 (w/o Met) A.A. GVTGWRLCKRESA 297 NLpep40 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCCGGAGCGCG 298 NLpep40 (w/o Met) A.A. GVTGWRLCKRRSA 299 NLpep41 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCTTCAGCGCG 300 NLpep41 (w/o Met) A.A. GVTGWRLCKRFSA 301 NLpep42 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCAAC 302 NLpep42 (w/o Met) A.A. GVTGWRLCKRISN 303 NLpep43 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCACC 304 NLpep43 (w/o Met) A.A. GVTGWRLCKRIST 305 NLpep44 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCCGG 306 NLpep44 (w/o Met) A.A. GVTGWRLCKRISR 307 NLpep45 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCCTG 308 NLpep45 (w/o Met) A.A. GVTGWRLCKRISL 309 NLpep46 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGAG 310 NLpep46 (w/o Met) A.A. GVTGWRLCKRISE 311 NLpep47 (w/o Met) N.A. GGAGTGACCGGCTTCCGGCTGTGCAAGCGCATTAGCGCG 312 NLpep47 (w/o Met) A.A. GVTGFRLCKRISA 313 NLpep48 (w/o Met) N.A. GGAGTGACCGGCTACCGGCTGTGCAAGCGCATTAGCGCG 314 NLpep48 (w/o Met) A.A. GVTGYRLCKRISA 315 NLpep49(w/o Met) N.A. GGAGTGACCGGCGAGCGGCTGTGCAAGCGCATTAGCGCG 316 NLpep49(w/o Met) A.A. GVTGERLCKRISA 317 NLpep50 (w/o Met) N.A. CAGGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 318 NLpep50 (w/o Met) A.A. QVTGWRLCKRISA 319 NLpep51 (w/o Met) N.A. ACCGTGACCGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 320 NLpep51 (w/o Met) A.A. TVTGWRLCKRISA 321 NLpep52 (w/o Met) N.A. GGAGTGGAGGGCTGGCGGCTGTGCAAGCGCATTAGCGCG 322 NLpep52 (w/o Met) A.A. GVEGWRLCKRISA 323 NLpep53 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 324 NLpep53 (w/o Met) A.A. GVTGWRLFKRISA 325 NLpep54 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTACAAGCGCATTAGCGCG 326 NLpep54 (w/o Met) A.A. GVTGWRLYKRISA 327 NLpep55 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGAGCAAGCGCATTAGCGCG 328 NLpep55 (w/o Met) A.A. GVTGWRLSKRISA 329 NLpep56 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGGGCAAGCGCATTAGCGCG 330 NLpep56 (w/o Met) A.A. GVTGWRLHKRISA 331 NLpep57 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGATGAAGCGCATTAGCGCG 332 NLpep57 (w/o Met) A.A. GVTGWRLMKRISA 333 NLpep58 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGGCCAAGCGCATTAGCGCG 334 NLpep58 (w/o Met) A.A. GVTGWRLAKRISA 335 NLpep59 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGCAGAAGCGCATTAGCGCG 336 NLpep59 (w/o Met) A.A. GVTGWRLQKRISA 337 NLpep60 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGCTGAAGCGCATTAGCGCG 338 NLpep60 (w/o Met) A.A. GVTGWRLLKRISA 339 NLpep61 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGAAGAAGCGCATTAGCGCG 340 NLpep61 (w/o Met) A.A. GVTGWRLKKRISA 341 NLpep62 (w/o Met) N.A. AACCACACCGGCTGGCGGCTGAACAAGAAGGTGAGCAAC 342 NLpep62 (w/o Met) A.A. NITGWRLNKKVSN 343 NLpep63 (w/o Met) N.A. AACCACACCGGCTACCGGCTGAACAAGAAGGTGAGCAAC 344 NLpep63 (w/o Met) A.A. NITGYRLNKKVSN 345 NLpep64 (w/o Met) N.A. TGCGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 346 NLpep64 (w/o Met) A.A. CVTGWRLFKRISA 347 NLpep65 (w/o Met) N.A. CCCGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 348 NLpep65 (w/o Met) A.A. PVTGWRLFKRISA 349 NLpep66 (w/o Met) N.A. AACCACACCGGCTACCGGCTGTTCAAGAAGGTGAGCAAC 350 NLpep66 (w/o Met) A.A. NITGYRLFKKVSN 351 NLpep67 (w/o Met) N.A. AACGTGACCGGCTACCGGCTGTTCAAGAAGGTGAGCAAC 352 NLpep67 (w/o Met) A.A. NVTGYRLFKKVSN 353 NLpep68 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCAAGAAGGTGAGCAAC 354 NLpep68 (w/o Met) A.A. NVTGWRLFKKVSN 355 NLpep69 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 356 NLpep69 (w/o Met) A.A. NVTGWRLFKKISN 357 NLpep70 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCAAC 358 NLpep70 (w/o Met) A.A. NVTGWRLFKRISN 359 NLpep71 (w/o Met) N.A. GGAGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCAAC 360 NLpep71 (w/o Met) A.A. GVTGWRLFKRISN 361 NLpep72 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCGAACGCATTAGCAAC 362 NLpep72 (w/o Met) A.A. NVTGWRLFERISN 363 NLpep73 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCAAGCGCATTCTGAAC 364 NLpep73 (w/o Met) A.A. NVTGWRLFKRILN 365 NLpep74 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCAAGCGCATTAGCGCG 366 NLpep74 (w/o Met) A.A. NVTGWRLFKRISA 367 NLpep75 (w/o Met) N.A. AACGTGACCGGCTGGCGGCTGTTCGAAAAGATTAGCAAC 368 NLpep75 (w/o Met) A.A. NVTGWRLFEKISN 369 NLpep76 (w/o Met) N.A. AACGTGAGCGGCTGGCGGCTGTTCGAAAAGATTAGCAAC 370 NLpep76 (w/o Met) A.A. NVSGWRLFEKISN 371 NLpep77 (w/o Met) N.A. GTGACCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 372 NLpep77 (w/o Met) A.A. VTGWRLFKKISN 373 NLpep78 (w/o Met) N.A. AACGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 374 NLpep78 (w/o Met) A.A. NVSGWRLFKKISN 375 NLpep79 (w/o Met) N.A. AACGTGACCGGCTACCGGCTGTTCAAGAAGATTAGCAAC 376 NLpep79 (w/o Met) A.A. NVTGYRLFKKISN 377 NLpep80(w/o Met) N.A. GTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 378 NLpep80(w/o Met) A.A. VSGWRLFKKISN 379 NLpep81 (w/o Met) N.A. AGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 380 NLpep81 (w/o Met) A.A. SGWRLFKKISN 381 NLpep82 (w/o Met) N.A. GGCTGGCGGCTGTTCAAGAAGATTAGCAAC 382 NLpep82 (w/o Met) A.A. GWRLFKKISN 383 NLpep83 (w/o Met) N.A. AACGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGC 384 NLpep83 (w/o Met) A.A. NVSGWRLFKKIS 385 NLpep84 (w/o Met) N.A. AACGTGAGCGGCTGGCGGCTGTTCAAGAAGATT 386 NLpep84 (w/o Met) A.A. NVSGWRLFKKI 387 NLpep85 (w/o Met) N.A. AACGTGAGCGGCTGGCGGCTGTTCAAGAAG 388 NLpep85 (w/o Met) A.A. NVSGWRLFKK 389 NLpep86 (w/o Met) N.A. GTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGC 390 NLpep86 (w/o Met) A.A. VSGWRLFKKIS 391 NLpep87 (w/o Met) N.A. AGCGGCTGGCGGCTGTTCAAGAAGATT 392 NLpep87 (w/o Met) A.A. SGWRLFKKI 393 NLpep88 (w/o Met) N.A. AACGTGAGCGGCTGGGGCCTGTTCAAGAAGATTAGCAAC 394 NLpep88 (w/o Met) A.A. NVSGWGLFKKISN 395 NLpep89 (w/o Met) N.A. CCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 396 NLpep89 (w/o Met) A.A. PVSGWRLFKKISN 397 NLpep90 (w/o Met) N.A. AACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 398 NLpep90 (w/o Met) A.A. NPVSGWRLFKKISN 399 NLpep91 (w/o Met) N.A. ATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCAAC 400 NLpep91 (w/o Met) A.A. INPVSGWRLFKKISN 401 NLpep92 (w/o Met) N.A. ACCATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTAGCA AC 402 NLpep92 (w/o Met) A.A. TINPVSGWRLFKKISN 403 NLpep93 (w/o Met) N.A. GTGACCATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAGATTA GCAAC 404 NLpep93 (w/o Met) A.A. VTINPVSGWRLFKKISN 405 NLpep94 (w/o Met) N.A. CGGGTGACCATCAACCCCGTGAGCGGCTGGCGGCTGTTCAAGAAG ATTAGCAAC 406 NLpep94 (w/o Met) A.A. RVTINPVSGWRLFKKISN 407 NLpep95 (w/o Met) N.A. AGCGGCTGGCGGCTGCTGAAGAAGATT 408 NLpep95 (w/o Met) A.A. SGWRLLKKI 409 NLpep96 (w/o Met) N.A. ACCGGCTACCGGCTGCTGAAGAAGATT 410 NLpep96 (w/o Met) A.A. TGYRLLKKI 411 NLpep97 (w/o Met) N.A. AGCGGCTGGCGGCTGTTCAAGAAG 412 NLpep97 (w/o Met) A.A. SGWRLFKK 413 NLpep98 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCAAGAAGATTAGC 414 NLpep98 (w/o Met) A.A. VTGYRLFKKIS 415 NLpep99 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGAAGATTAGC 416 NLpep99 (w/o Met) A.A. VTGYRLFEKIS 417 NLpep100 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGCAGATTAGC 418 NLpep100 (w/o Met) A.A. VTGYRLFEQIS 419 NLpep101 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGAAGGAGAGC 420 NLpep101 (w/o Met) A.A. VTGYRLFEKES 421 NLpep102 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGCAGGAGAGC 422 NLpep102 (w/o Met) A.A. VTGYRLFEQES 423 NLpep103 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGCAGGAGCTG 424 NLpep103 (w/o Met) A.A. VTGYRLFEQEL 425 NLpep104 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGAAGATTAGC 426 NLpep104 (w/o Met) A.A. VEGYRLFEKIS 427 NLpep105 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGCAGATTAGC 428 NLpep105 (w/o Met) A.A. VEGYRLFEQIS 429 NLpep106 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGAAGGAGAGC 430 NLpep106 (w/o Met) A.A. VEGYRLFEKES 431 NLpep107 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGCAGGAGAGC 432 NLpep107 (w/o Met) A.A. VEGYRLFEQES 433 NLpep108 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGCAGGAGCTG 434 NLpep108 (w/o Met) A.A. VEGYRLFEQEL 435 NLpep109 (w/o Met) N.A. ATTAGCGGCTGGCGGCTGATGAAGAACATTAGC 436 NLpep109 (w/o Met) A.A. ISGWRLMKNIS 437 NLpep110 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCAAGAAGATTAGC 438 NLpep110 (w/o Met) A.A. VEGYRLFKKIS 2162 NLpep111 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGATCAGC 2163 NLpep111 (w/ Met) A.A. MVTGYRLFEEIS 2164 NLpep112 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGGCCAGC 2165 NLpep112 (w/ Met) A.A. MVTGYRLFEEAS 2166 NLpep113 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGGAGAGC 2167 NLpep113 (w/ Met) A.A. MVTGYRLFEEES 2168 NLpep114 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGATCCTG 2169 NLpep114 (w/ Met) A.A. MVTGYRLFEEIL 2170 NLpep115 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGGCCCTG 2171 NLpep115 (w/ Met) A.A. MVTGYRLFEEAL 2172 NLpep116 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGGAGCTG 2173 NLpep116 (w/ Met) A.A. MVTGYRLFEEEL 2174 NLpep117 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGGAGATCAGC 2175 NLpep117 (w/ Met) A.A. MVEGYRLFEEIS 2176 NLpep118 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGGAGGCCAGC 2177 NLpep118 (w/ Met) A.A. MVEGYRLFEEAS 2178 NLpep119 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGGAGGAGAGC 2179 NLpep119 (w/ Met) A.A. MVEGYRLFEEES 2180 NLpep120 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGGAGATCCTG 2181 NLpep120 (w/ Met) A.A. MVEGYRLFEEIL 2182 NLpep121 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGGAGGCCCTG 2183 NLpep121 (w/ Met) A.A. MVEGYRLFEEAL 2184 NLpep122 (w/ Met) N.A. ATGGTGGAGGGCTACCGGCTGTTCGAGGAGGAGCTG 2185 NLpep122 (w/ Met) A.A. MVEGYRLFEEEL 2186 NLpep123 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCAAGAAGATCCTG 2187 NLpep123 (w/ Met) A.A. MVTGYRLFKKIL 2188 NLpep124 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGATGAAGAAGATCCTG 2189 NLpep124 (w/ Met) A.A. MVTGYRLMKKIL 2190 NLpep125 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGCACAAGAAGATCCTG 2191 NLpep125 (w/ Met) A.A. MVTGYRLHKKIL 2192 NLpep126 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGCTGAAGAAGATCCTG 2193 NLpep126 (w/ Met) A.A. MVTGYRLLKKIL 2194 NLpep127 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGAGCAAGAAGATCCTG 2195 NLpep127 (w/ Met) A.A. MVTGYRLSKKIL 2196 NLpep128 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGAAGATCCTG 2197 NLpep128 (w/ Met) A.A. MVTGYRLFEKIL 2198 NLpep129(w/ Met) N.A. ATGGTGACCGGCTACCGGCTGATGGAGAAGATCCTG 2199 NLpep129(w/ Met) A.A. MVTGYRLMEKIL 2200 NLpep130 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGCACGAGAAGATCCTG 2201 NLpep130 (w/ Met) A.A. MVTGYRLHEKIL 2202 NLpep131 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGCTGGAGAAGATCCTG 2203 NLpep131 (w/ Met) A.A. MVTGYRLLEKIL 2204 NLpep132 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGAGCGAGAAGATCCTG 2205 NLpep132 (w/ Met) A.A. MVTGYRLSEKIL 2206 NLpep133 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGATGGAGGAGATCCTG 2207 NLpep133 (w/ Met) A.A. MVTGYRLMEEIL 2208 NLpep134(w/ Met) N.A. ATGGTGACCGGCTACCGGCTGCACGAGGAGATCCTG 2209 NLpep134(w/ Met) A.A. MVTGYRLHEEIL 2210 NLpep135 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGCTGGAGGAGATCCTG 2211 NLpep135 (w/ Met) A.A. MVTGYRLLEEIL 2212 NLpep136 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGAGCGAGGAGATCCTG 2213 NLpep136 (w/ Met) A.A. MVTGYRLSEEIL 2214 NLpep137(w/ Met) N.A. ATGGTGAGCGGCTACCGGCTGTTCGAGGAGATCCTG 2215 NLpep137(w/ Met) A.A. MVSGYRLFEEIL 2216 NLpep138(w/ Met) N.A. ATGGTGACCGGCTGGCGGCTGTTCGAGGAGATCCTG 2217 NLpep138(w/ Met) A.A. MVTGWRLFEEIL 2218 NLpep139 (w/ Met) N.A. ATGGTGAGCGGCTGGCGGCTGTTCGAGGAGATCCTG 2219 NLpep139 (w/ Met) A.A. MVSGWRLFEEIL 2220 NLpep140 (w/ Met) N.A. ATGAACGTGACCGGCTACCGGCTGTTCGAGGAGATCCTG 2221 NLpep140 (w/ Met) A.A. MNVTGYRLFEEIL 2222 NLpep141 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGATCCTGAAC 2223 NLpep141 (w/ Met) A.A. MVTGYRLFEEILN 2224 NLpep142 (w/ Met) N.A. ATGAACGTGACCGGCTACCGGCTGTTCGAGGAGATCCTGAAC 2225 NLpep142 (w/ Met) A.A. MNVTGYRLFEEILN 2226 NLpep143 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCGAGGAGATC 2227 NLpep143 (w/ Met) A.A. MVTGYRLFEEI 2228 NLpep144 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCCAGAAGATCAGC 2229 NLpep144 (w/ Met) A.A. MVTGYRLFQKIS 2230 NLpep145 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCAAGAAGATCAGCAAC 2231 NLpep145 (w/ Met) A.A. MVTGYRLFKKISN 2232 NLpep146 (w/ Met) N.A. ATGGTGACCGGCTACCGGCTGTTCAAGAAGATCAGC 2233 NLpep146 (w/ Met) A.A. MVTGYRLFKKIS 2234 NLpep147 (w/ Met) A.A. MVSGWRLFKKISA 2235 NLpep148 (w/ Met) A.A. MGVSGWRLFKKIS 2236 NLpep149 (w/ Met) A.A. MSVSGWRLFKKISN 2237 NLpep150 (w/ Met) A.A. MSVSGWRLFKKISA 2238 NLpep151 (w/ Met) A.A. MNSVSGWRLFKKISA 2239 NLpep152 (w/ Met) A.A. MNSVSGWRLFKKISN 2240 NLpep153 (w/ Met) A.A. MSNVSGWRLFKKIS 2241 NLpep154 (w/ Met) A.A. MSGVSGWRLFKKIS 2242 NLpep155 (w/ Met) A.A. MNSNVSGWRLFKKIS 2243 NLpep156 (w/ Met) A.A. MNSGVSGWRLFKKIS 2244 NLpep157 (w/ Met) A.A. MSVSGWRLFKKIS 2245 NLpep158 (w/ Met) A.A. MNSVSGWRLFKKIS 2246 NLpep159 (w/ Met) A.A. MSNVSGWRLFKKISN 2247 NLpep160 (w/ Met) A.A. MNSNVSGWRLFKKISN 2248 NLpep161 (w/ Met) A.A. MGWRLFKK 2249 NLpep162(w/ Met) A.A. MGWALFKK 2250 NLpep163 (w/ Met) A.A. MVTGWALFEEIL 2251 NLpep164 (w/ Met) A.A. MVTGYALFQEIL 2252 NLpep165 (w/ Met) A.A. MVTGYALFEQIL 2253 NLpep166 (w/ Met) A.A. MVTGYALFEEIL 2254 NLpep167 (w/ Met) N.A. ATGGTGTCCGGCTGGGCACTGTTCAAGAAAATTTCC 2255 NLpep167 (w/ Met) A.A. MVSGWALFKKIS 2256 NLpep168 (w/ Met) A.A. MVSGWKLFKKIS 2257 NLpep169 (w/ Met) N.A. ATGGTGTCCGGCTGGCAGCTGTTCAAGAAAATTTCC 2258 NLpep169 (w/ Met) A.A. MVSGWQLFKKIS 2259 NLpep170 (w/ Met) A.A. MVSGWELFKKIS 2260 NLpep171 (w/ Met) N.A. ATGGTGTCCGGCTGGCTGCTGTTCAAGAAAATTTCC 2261 NLpep171 (w/ Met) A.A. MVSGWLLFKKIS 2262 NLpep172(w/ Met) N.A. ATGGTGTCCGGCTGGGTGCTGTTCAAGAAAATTTCC 2263 NLpep172(w/ Met) A.A. MVSGWVLFKKIS 2264 NLpep111 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGATCAGC 2265 NLpep111 (w/o Met) A.A. VTGYRLFEEIS 2266 NLpep112 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGGCCAGC 2267 NLpep112 (w/o Met) A.A. VTGYRLFEEAS 2268 NLpep113 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGGAGAGC 2269 NLpep113 (w/o Met) A.A. VTGYRLFEEES 2270 NLpep114 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGATCCTG 2271 NLpep114 (w/o Met) A.A. VTGYRLFEEIL 2272 NLpep115 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGGCCCTG 2273 NLpep115 (w/o Met) A.A. VTGYRLFEEAL 2274 NLpep116 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGGAGCTG 2275 NLpep116 (w/o Met) A.A. VTGYRLFEEEL 2276 NLpep117 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGGAGATCAGC 2277 NLpep117 (w/o Met) A.A. VEGYRLFEEIS 2278 NLpep118 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGGAGGCCAGC 2279 NLpep118 (w/o Met) A.A. VEGYRLFEEAS 2280 NLpep119 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGGAGGAGAGC 2281 NLpep119 (w/o Met) A.A. VEGYRLFEEES 2282 NLpep120 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGGAGATCCTG 2283 NLpep120 (w/o Met) A.A. VEGYRLFEEIL 2284 NLpep121 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGGAGGCCCTG 2285 NLpep121 (w/o Met) A.A. VEGYRLFEEAL 2286 NLpep122 (w/o Met) N.A. GTGGAGGGCTACCGGCTGTTCGAGGAGGAGCTG 2287 NLpep122 (w/o Met) A.A. VEGYRLFEEEL 2288 NLpep123 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCAAGAAGATCCTG 2289 NLpep123 (w/o Met) A.A. VTGYRLFKKIL 2290 NLpep124 (w/o Met) N.A. GTGACCGGCTACCGGCTGATGAAGAAGATCCTG 2291 NLpep124 (w/o Met) A.A. VTGYRLMKKIL 2292 NLpep125 (w/o Met) N.A. GTGACCGGCTACCGGCTGCACAAGAAGATCCTG 2293 NLpep125 (w/o Met) A.A. VTGYRLHKKIL 2294 NLpep126 (w/o Met) N.A. GTGACCGGCTACCGGCTGCTGAAGAAGATCCTG 2295 NLpep126 (w/o Met) A.A. VTGYRLLKKIL 2296 NLpep127 (w/o Met) N.A. GTGACCGGCTACCGGCTGAGCAAGAAGATCCTG 2297 NLpep127 (w/o Met) A.A. VTGYRLSKKIL 2298 NLpep128 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGAAGATCCTG 2299 NLpep128 (w/o Met) A.A. VTGYRLFEKIL 2300 NLpep129(w/o Met) N.A. GTGACCGGCTACCGGCTGATGGAGAAGATCCTG 2301 NLpep129(w/o Met) A.A. VTGYRLMEKIL 2302 NLpep130 (w/o Met) N.A. GTGACCGGCTACCGGCTGCACGAGAAGATCCTG 2303 NLpep130 (w/o Met) A.A. VTGYRLHEKIL 2304 NLpep131 (w/o Met) N.A. GTGACCGGCTACCGGCTGCTGGAGAAGATCCTG 2305 NLpep131 (w/o Met) A.A. VTGYRLLEKIL 2306 NLpep132 (w/o Met) N.A. GTGACCGGCTACCGGCTGAGCGAGAAGATCCTG 2307 NLpep132 (w/o Met) A.A. VTGYRLSEKIL 2308 NLpep133 (w/o Met) N.A. GTGACCGGCTACCGGCTGATGGAGGAGATCCTG 2309 NLpep133 (w/o Met) A.A. VTGYRLMEEIL 2310 NLpep134(w/o Met) N.A. GTGACCGGCTACCGGCTGCACGAGGAGATCCTG 2311 NLpep134(w/o Met) A.A. VTGYRLHEEIL 2312 NLpep135 (w/o Met) N.A. GTGACCGGCTACCGGCTGCTGGAGGAGATCCTG 2313 NLpep135 (w/o Met) A.A. VTGYRLLEEIL 2314 NLpep136 (w/o Met) N.A. GTGACCGGCTACCGGCTGAGCGAGGAGATCCTG 2315 NLpep136 (w/o Met) A.A. VTGYRLSEEIL 2316 NLpep137(w/o Met) N.A. GTGAGCGGCTACCGGCTGTTCGAGGAGATCCTG 2317 NLpep137(w/o Met) A.A. VSGYRLFEEIL 2318 NLpep138(w/o Met) N.A. GTGACCGGCTGGCGGCTGTTCGAGGAGATCCTG 2319 NLpep138(w/o Met) A.A. VTGWRLFEEIL 2320 NLpep139 (w/o Met) N.A. GTGAGCGGCTGGCGGCTGTTCGAGGAGATCCTG 2321 NLpep139 (w/o Met) A.A. VSGWRLFEEIL 2322 NLpep140 (w/o Met) N.A. AACGTGACCGGCTACCGGCTGTTCGAGGAGATCCTG 2323 NLpep140 (w/o Met) A.A. NVTGYRLFEEIL 2324 NLpep141 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGATCCTGAAC 2325 NLpep141 (w/o Met) A.A. VTGYRLFEEILN 2326 NLpep142 (w/o Met) N.A. AACGTGACCGGCTACCGGCTGTTCGAGGAGATCCTGAAC 2327 NLpep142 (w/o Met) A.A. NVTGYRLFEEILN 2328 NLpep143 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCGAGGAGATC 2329 NLpep143 (w/o Met) A.A. VTGYRLFEEI 2330 NLpep144 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCCAGAAGATCAGC 2331 NLpep144 (w/o Met) A.A. VTGYRLFQKIS 2332 NLpep145 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCAAGAAGATCAGCAAC 2333 NLpep145 (w/o Met) A.A. VTGYRLFKKISN 2334 NLpep146 (w/o Met) N.A. GTGACCGGCTACCGGCTGTTCAAGAAGATCAGC 2335 NLpep146 (w/o Met) A.A. VTGYRLFKKIS 2336 NLpep147 (w/o Met) A.A. VSGWRLFKKISA 2337 NLpep148 (w/o Met) A.A. GVSGWRLFKKIS 2338 NLpep149 (w/o Met) A.A. SVSGWRLFKKISN 2339 NLpep150 (w/o Met) A.A. SVSGWRLFKKISA 2340 NLpep151 (w/o Met) A.A. NSVSGWRLFKKISA 2341 NLpep152 (w/o Met) A.A. NSVSGWRLFKKISN 2342 NLpep153 (w/o Met) A.A. SNVSGWRLFKKIS 2343 NLpep154 (w/o Met) A.A. SGVSGWRLFKKIS 2344 NLpep155 (w/o Met) A.A. NSNVSGWRLFKKIS 2345 NLpep156 (w/o Met) A.A. NSGVSGWRLFKKIS 2346 NLpep157 (w/o Met) A.A. SVSGWRLFKKIS 2347 NLpep158 (w/o Met) A.A. NSVSGWRLFKKIS 2348 NLpep159 (w/o Met) A.A. SNVSGWRLFKKISN 2349 NLpep160 (w/o Met) A.A. NSNVSGWRLFKKISN 2350 NLpep161 (w/o Met) A.A. GWRLFKK 2351 NLpep162(w/o Met) A.A. GWALFKK 2352 NLpep163 (w/o Met) A.A. VTGWALFEEIL 2353 NLpep164 (w/o Met) A.A. VTGYALFQEIL 2354 NLpep165 (w/o Met) A.A. VTGYALFEQIL 2355 NLpep166 (w/o Met) A.A. VTGYALFEEIL 2356 NLpep167 (w/o Met) N.A. GTGTCCGGCTGGGCACTGTTCAAGAAAATTTCC 2357 NLpep167 (w/o Met) A.A. VSGWALFKKIS 2358 NLpep168 (w/o Met) A.A. VSGWKLFKKIS 2359 NLpep169 (w/o Met) N.A. GTGTCCGGCTGGCAGCTGTTCAAGAAAATTTCC 2360 NLpep169 (w/o Met) A.A. VSGWQLFKKIS 2361 NLpep170 (w/o Met) A.A. VSGWELFKKIS 2362 NLpep171 (w/o Met) N.A. GTGTCCGGCTGGCTGCTGTTCAAGAAAATTTCC 2363 NLpep171 (w/o Met) A.A. VSGWLLFKKIS 2364 NLpep172(w/o Met) N.A. GTGTCCGGCTGGGTGCTGTTCAAGAAAATTTCC 2365 NLpep172(w/o Met) A.A. VSGWVLFKKIS

In certain embodiments, a peptide from Table 1 is provided (e.g., as an internal tag or a structural complement of an internal tag). In some embodiments, an internal tag or a structural complement comprise a single amino acid difference from GVTGWRLCKRILA (SEQ ID NO: 2) and/or any of the peptides listed in Table 1. In some embodiments, an internal tag or a structural complement comprises two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) amino acid differences from GVTGWRLCKRILA (SEQ ID NO: 2) and/or any of the peptides listed in Table 1. In some embodiments, an internal tag or a structural complement is provided comprising one of the amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365. In some embodiments, an internal tag or a structural complement is provided comprising one of the amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365 with one or more additions, substitutions, and/or deletions. In some embodiments, an internal tag, a structural complement, or a portion thereof comprises greater than 70% sequence identity (e.g., 71%, 75%, 80%, 85%, 90%, 95%, 99%) with one or more of the amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365. In some embodiments, nucleic acids are provided comprising one of the nucleic acid coding sequences of SEQ ID NOS: 3-438 and 2162-2365. In some embodiments, nucleic acids are provided comprising one of the nucleic acid sequences of SEQ ID NOS: 3-438 and 2162-2365 with one or more additions, substitutions, and/or deletions. In some embodiments, a nucleic acid or a portion thereof comprises greater than 70% sequence identity (e.g., 71%, 75%, 80%, 85%, 90%, 95%, 99%) with one or more of the nucleic acid sequence of SEQ ID NOS: 3-438 and 2162-2365. In some embodiments, nucleic acids are provided that code for one of the amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365. In some embodiments, nucleic acids are provided that code for one of the amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365 with one or more additions, substitutions, and/or deletions. In some embodiments, a nucleic acid is provided that codes for an amino acid with greater than 70% sequence identity (e.g., 71%, 75%, 80%, 85%, 90%, 95%, 99%) with one or more of the amino acid sequences of SEQ ID NOS: 3-438 and 2162-2365.

In certain embodiments, a nucleic acid from Table 1 is provided. In some embodiments, a nucleic acid encoding a peptide from Table 1 is provided. In some embodiments, a nucleic acid encoding a peptide from Table 1 inserted into another polypeptide sequence is provided. In some embodiments, a nucleic acid of the present invention codes for a peptide that comprises a single amino acid difference from MGVTGWRLCERILA (SEQ ID NO: 2) and/or any of the peptides listed in Table 1 (e.g., inserted into a polypeptide sequence). In some embodiments, nucleic acids code for peptides comprising two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) amino acid differences from MGVTGWRLCERILA (SEQ ID NO: 2) and/or any of the peptides listed in Table 1 (e.g., inserted into a polypeptide sequence). In some embodiments, nucleic acids are provided comprising the sequence of one of the nucleic acids in Table 1 (e.g., inserted into a polypeptide sequence). In some embodiments, nucleic acids are provided comprising one of the nucleic acids of Table 1 with one or more additions, substitutions, and/or deletions. In some embodiments, a nucleic acid or a portion thereof comprises greater than 70% sequence identity (e.g., 71%, 75%, 80%, 85%, 90%, 95%, 99%) with one or more of the nucleic acids of Table 1 (e.g., inserted into a polypeptide sequence).

In some embodiments, internal tags and/or a structural complements of an internal tag that find use in embodiments described herein include polypeptides with one or more amino acid substitutions, deletions, or additions from SEQ ID NO: 440. In some embodiments provided herein is an internal tag or a structural complement of an internal tag comprising an amino acid sequence of Table 2, and/or nucleic acids comprising the nucleic acid sequences of Table 2.

TABLE 2 Exemplary internal tag and/or structural complement polypeptide sequences SEQ SEQ SEQ ID ID ID NO Polymer ID NO Poly. ID NO Poly. ID 441 N.A. R11N 727 N.A. 5A2 + V58P 1013 N.A. 5P D6 (−152-157) 442 A.A R11N 728 A.A 5A2 + V58P 1014 A.A 5P D6 (−152-157) 443 N.A. T13I 729 N.A. 5A2 + V58Q 1015 N.A. 5P D7 (−151-157) 444 A.A T13I 730 A.A 5A2 + V58Q 1016 A.A 5P D7 (−151-157) 445 N.A. G15S 731 N.A. 5A2 + V58R 1017 N.A. 5P + F31A 446 A.A G15S 732 A.A 5A2 + V58R 1018 A.A 5P + F31A 447 N.A. L18Q 733 N.A. 5A2 + V58S 1019 N.A. 5P + F31C 448 A.A L18Q 734 A.A 5A2 + V58S 1020 A.A 5P + F31C 449 N.A. Q20K 735 N.A. 5A2 + V58T 1021 N.A. 5P + F31D 450 A.A Q20K 736 A.A 5A2 + V58T 1022 A.A 5P + F31D 451 N.A. V27M 737 N.A. 5A2 + V58W 1023 N.A. 5P + F31E 452 A.A V27M 738 A.A 5A2 + V58W 1024 A.A 5P + F31E 453 N.A. F31I 739 N.A. 5A2 + V58Y 1025 N.A. 5P + F31G 454 A.A F31I 740 A.A 5A2 + V58Y 1026 A.A 5P + F31G 455 N.A. F31L 741 N.A. 5A2 + A67C 1027 N.A. 5P + F31H 456 A.A F31L 742 A.A 5A2 + A67C 1028 A.A 5P + F31H 457 N.A. F31V 743 N.A. 5A2 + A67D 1029 N.A. 5P + F31I 458 A.A F31V 744 A.A 5A2 + A67D 1030 A.A 5P + F31I 459 N.A. Q32R 745 N.A. 5A2 + A67E 1031 N.A. 5P + F31K 460 A.A Q32R 746 A.A 5A2 + A67E 1032 A.A 5P + F31K 461 N.A. N33K 747 N.A. 5A2 + A67F 1033 N.A. 5P + F31L 462 A.A N33K 748 A.A 5A2 + A67F 1034 A.A 5P + F31L 463 N.A. N33R 749 N.A. 5A2 + A67G 1035 N.A. 5P + F31M 464 A.A N33R 750 A.A 5A2 + A67G 1036 A.A 5P + F31M 465 N.A. I56N 751 N.A. 5A2 + A67H 1037 N.A. 5P + F31N 466 A.A I56N 752 A.A 5A2 + A67H 1038 A.A 5P + F31N 467 N.A. V58A 753 N.A. 5A2 + A67I 1039 N.A. 5P + F31P 468 A.A V58A 754 A.A 5A2 + A67I 1040 A.A 5P + F31P 469 N.A. I59T 755 N.A. 5A2 + A67K 1041 N.A. 5P + F31Q 470 A.A I59T 756 A.A 5A2 + A67K 1042 A.A 5P + F31Q 471 N.A. G67S 757 N.A. 5A2 + A67L 1043 N.A. 5P + F31R 472 A.A G67S 758 A.A 5A2 + A67L 1044 A.A 5P + F31R 473 N.A. G67D 759 N.A. 5A2 + A67M 1045 N.A. 5P + F31S 474 A.A G67D 760 A.A 5A2 + A67M 1046 A.A 5P + F31S 475 N.A. K75E 761 N.A. 5A2 + A67N 1047 N.A. 5P + F31T 476 A.A K75E 762 A.A 5A2 + A67N 1048 A.A 5P + F31T 477 N.A. M106V 763 N.A. 5A2 + A67P 1049 N.A. 5P + F31V 478 A.A M106V 764 A.A 5A2 + A67P 1050 A.A 5P + F31V 479 N.A. M106I 765 N.A. 5A2 + A67Q 1051 N.A. 5P + F31W 480 A.A M106I 766 A.A 5A2 + A67Q 1052 A.A 5P + F31W 481 N.A. D108N 767 N.A. 5A2 + A67R 1053 N.A. 5P + F31Y 482 A.A D108N 768 A.A 5A2 + A67R 1054 A.A 5P + F31Y 483 N.A. R112Q 769 N.A. 5A2 + A67S 1055 N.A. 5P + L46A 484 A.A R112Q 770 A.A 5A2 + A67S 1056 A.A 5P + L46A 485 N.A. N144T 771 N.A. 5A2 + A67T 1057 N.A. 5P + L46C 486 A.A N144T 772 A.A 5A2 + A67T 1058 A.A 5P + L46C 487 N.A. L149M 773 N.A. 5A2 + A67V 1059 N.A. 5P + L46D 488 A.A L149M 774 A.A 5A2 + A67V 1060 A.A 5P + L46D 489 N.A. N156D 775 N.A. 5A2 + A67W 1061 N.A. 5P + L46E 490 A.A N156D 776 A.A 5A2 + A67W 1062 A.A 5P + L46E 491 N.A. N156S 777 N.A. 5A2 + A67Y 1063 N.A. 5P + L46F 492 A.A N156S 778 A.A 5A2 + A67Y 1064 A.A 5P + L46F 493 N.A. V157D 779 N.A. 5A2 + M106A 1065 N.A. 5P + L46G 494 A.A V157D 780 A.A 5A2 + M106A 1066 A.A 5P + L46G 495 N.A. V157S 781 N.A. 5A2 + M106C 1067 N.A. 5P + L46H 496 A.A V157S 782 A.A 5A2 + M106C 1068 A.A 5P + L46H 497 N.A. G8A 783 N.A. 5A2 + M106D 1069 N.A. 5P + L46I 498 A.A G8A 784 A.A 5A2 + M106D 1070 A.A 5P + L46I 499 N.A. G15A 785 N.A. 5A2 + M106E 1071 N.A. 5P + L46K 500 A.A G15A 786 A.A 5A2 + M106E 1072 A.A 5P + L46K 501 N.A. G25A 787 N.A. 5A2 + M106F 1073 N.A. 5P + L46M 502 A.A G25A 788 A.A 5A2 + M106F 1074 A.A 5P + L46M 503 N.A. G26A 789 N.A. 5A2 + M106G 1075 N.A. 5P + L46N 504 A.A G26A 790 A.A 5A2 + M106G 1076 A.A 5P + L46N 505 N.A. G35A 791 N.A. 5A2 + M106H 1077 N.A. 5P + L46P 506 A.A G35A 792 A.A 5A2 + M106H 1078 A.A 5P + L46P 507 N.A. G48A 793 N.A. 5A2 + M106I 1079 N.A. 5P + L46Q 508 A.A G48A 794 A.A 5A2 + M106I 1080 A.A 5P + L46Q 509 N.A. G51A 795 N.A. 5A2 + M106K 1081 N.A. 5P + L46R 510 A.A G51A 796 A.A 5A2 + M106K 1082 A.A 5P + L46R 511 N.A. G64A 797 N.A. 5A2 + M106L 1083 N.A. 5P + L46S 512 A.A G64A 798 A.A 5A2 + M106L 1084 A.A 5P + L46S 513 N.A. G67A 799 N.A. 5A2 + M106N 1085 N.A. 5P + L46T 514 A.A G67A 800 A.A 5A2 + M106N 1086 A.A 5P + L46T 515 N.A. G71A 801 N.A. 5A2 + M106P 1087 N.A. 5P + L46V 516 A.A G71A 802 A.A 5A2 + M106P 1088 A.A 5P + L46V 517 N.A. G95A 803 N.A. 5A2 + M106Q 1089 N.A. 5P + L46W 518 A.A G95A 804 A.A 5A2 + M106Q 1090 A.A 5P + L46W 519 N.A. G101A 805 N.A. 5A2 + M106R 1091 N.A. 5P + L46Y 520 A.A G101A 806 A.A 5A2 + M106R 1092 A.A 5P + L46Y 521 N.A. G111A 807 N.A. 5A2 + M106S 1093 N.A. 5P + N108A 522 A.A G111A 808 A.A 5A2 + M106S 1094 A.A 5P + N108A 523 N.A. G116A 809 N.A. 5A2 + M106T 1095 N.A. 5P + N108C 524 A.A G116A 810 A.A 5A2 + M106T 1096 A.A 5P + N108C 525 N.A. G122A 811 N.A. 5A2 + M106V 1097 N.A. 5P + N108D 526 A.A G122A 812 A.A 5A2 + M106V 1098 A.A 5P + N108D 527 N.A. G129A 813 N.A. 5A2 + M106W 1099 N.A. 5P + N108E 528 A.A G129A 814 A.A 5A2 + M106W 1100 A.A 5P + N108E 529 N.A. G134A 815 N.A. 5A2 + M106Y 1101 N.A. 5P + N108F 530 A.A G134A 816 A.A 5A2 + M106Y 1102 A.A 5P + N108F 531 N.A. G147A 817 N.A. 5A2 + L149A 1103 N.A. 5P + N108G 532 A.A G147A 818 A.A 5A2 + L149A 1104 A.A 5P + N108G 533 N.A. I54A 819 N.A. 5A2 + L149C 1105 N.A. 5P + N108H 534 A.A I54A 820 A.A 5A2 + L149C 1106 A.A 5P + N108H 535 N.A. 5A1 821 N.A. 5A2 + L149D 1107 N.A. 5P + N108I (G15A/D19A/ G35A/G51A/G67A) 536 A.A 5A1 822 A.A 5A2 + L149D 1108 A.A 5P + N108I (G15A/D19A/ G35A/G51A/G67A) 537 N.A. 4A1 823 N.A. 5A2 + L149E 1109 N.A. 5P + N108K (G15A/G35A/ G67A/G71A) 538 A.A 4A1 824 A.A 5A2 + L149E 1110 A.A 5P + N108K (G15A/G35A/ G67A/G71A) 539 N.A. 5A2 825 N.A. 5A2 + L149F 1111 N.A. 5P + N108L (G15A/G35A/ G51A/G67A/G71A) 540 A.A 5A2 826 A.A 5A2 + L149F 1112 A.A 5P + N108L (G15A/G35A/ G51A/G67A/G71A) 541 N.A. 5A2 + A15G 827 N.A. 5A2 + L149G 1113 N.A. 5P + N108M 542 A.A 5A2 + A15G 828 A.A 5A2 + L149G 1114 A.A 5P + N108M 543 N.A. 5A2 + A35G 829 N.A. 5A2 + L149H 1115 N.A. 5P + N108P 544 A.A 5A2 + A35G 830 A.A 5A2 + L149H 1116 A.A 5P + N108P 545 N.A. 5A2 + A51G 831 N.A. 5A2 + L149I 1117 N.A. 5P + N108Q 546 A.A 5A2 + A51G 832 A.A 5A2 + L149I 1118 A.A 5P + N108Q 547 N.A. 5A2 + A67G 833 N.A. 5A2 + L149K 1119 N.A. 5P + N108R 548 A.A 5A2 + A67G 834 A.A 5A2 + L149K 1120 A.A 5P + N108R 549 N.A. 5A2 + A71G 835 N.A. 5A2 + L149M 1121 N.A. 5P + N108S 550 A.A 5A2 + A71G 836 A.A 5A2 + L149M 1122 A.A 5P + N108S 551 N.A. 5A2 + R11A 837 N.A. 5A2 + L149N 1123 N.A. 5P + N108T 552 A.A 5A2 + R11A 838 A.A 5A2 + L149N 1124 A.A 5P + N108T 553 N.A. 5A2 + R11C 839 N.A. 5A2 + L149P 1125 N.A. 5P + N108V 554 A.A 5A2 + R11C 840 A.A 5A2 + L149P 1126 A.A 5P + N108V 555 N.A. 5A2 + R11D 841 N.A. 5A2 + L149Q 1127 N.A. 5P + N108W 556 A.A 5A2 + R11D 842 A.A 5A2 + L149Q 1128 A.A 5P + N108W 557 N.A. 5A2 + R11E 843 N.A. 5A2 + L149R 1129 N.A. 5P + N108Y 558 A.A 5A2 + R11E 844 A.A 5A2 + L149R 1130 A.A 5P + N108Y 559 N.A. 5A2 + R11F 845 N.A. 5A2 + L149S 1131 N.A. 5P + T144A 560 A.A 5A2 + R11F 846 A.A 5A2 + L149S 1132 A.A 5P + T144A 561 N.A. 5A2 + R11G 847 N.A. 5A2 + L149T 1133 N.A. 5P + T144C 562 A.A 5A2 + R11G 848 A.A 5A2 + L149T 1134 A.A 5P + T144C 563 N.A. 5A2 + R11H 849 N.A. 5A2 + L149V 1135 N.A. 5P + T144D 564 A.A 5A2 + R11H 850 A.A 5A2 + L149V 1136 A.A 5P + T144D 565 N.A. 5A2 + R11I 851 N.A. 5A2 + L149W 1137 N.A. 5P + T144E 566 A.A 5A2 + R11I 852 A.A 5A2 + L149W 1138 A.A 5P + T144E 567 N.A. 5A2 + R11K 853 N.A. 5A2 + L149Y 1139 N.A. 5P + T144F 568 A.A 5A2 + R11K 854 A.A 5A2 + L149Y 1140 A.A 5P + T144F 569 N.A. 5A2 + R11L 855 N.A. 5A2 + V157A 1141 N.A. 5P + T144G 570 A.A 5A2 + R11L 856 A.A 5A2 + V157A 1142 A.A 5P + T144G 571 N.A. 5A2 + R11M 857 N.A. 5A2 + V157C 1143 N.A. 5P + T144H 572 A.A 5A2 + R11M 858 A.A 5A2 + V157C 1144 A.A 5P + T144H 573 N.A. 5A2 + R11N 859 N.A. 5A2 + V157D 1145 N.A. 5P + T144I 574 A.A 5A2 + R11N 860 A.A 5A2 + V157D 1146 A.A 5P + T144I 575 N.A. 5A2 + R11P 861 N.A. 5A2 + V157E 1147 N.A. 5P + T144K 576 A.A 5A2 + R11P 862 A.A 5A2 + V157E 1148 A.A 5P + T144K 577 N.A. 5A2 + R11Q 863 N.A. 5A2 + V157F 1149 N.A. 5P + T144L 578 A.A 5A2 + R11Q 864 A.A 5A2 + V157F 1150 A.A 5P + T144L 579 N.A. 5A2 + R11S 865 N.A. 5A2 + V157G 1151 N.A. 5P + T144M 580 A.A 5A2 + R11S 866 A.A 5A2 + V157G 1152 A.A 5P + T144M 581 N.A. 5A2 + R11T 867 N.A. 5A2 + V157H 1153 N.A. 5P + T144N 582 A.A 5A2 + R11T 868 A.A 5A2 + V157H 1154 A.A 5P + T144N 583 N.A. 5A2 + R11V 869 N.A. 5A2 + V157I 1155 N.A. 5P + T144P 584 A.A 5A2 + R11V 870 A.A 5A2 + V157I 1156 A.A 5P + T144P 585 N.A. 5A2 + R11W 871 N.A. 5A2 + V157K 1157 N.A. 5P + T144Q 586 A.A 5A2 + R11W 872 A.A 5A2 + V157K 1158 A.A 5P + T144Q 587 N.A. 5A2 + R11Y 873 N.A. 5A2 + V157L 1159 N.A. 5P + T144R 588 A.A 5A2 + R11Y 874 A.A 5A2 + V157L 1160 A.A 5P + T144R 589 N.A. 5A2 + A15C 875 N.A. 5A2 + V157M 1161 N.A. 5P + T144S 590 A.A 5A2 + A15C 876 A.A 5A2 + V157M 1440 A.A 5P + T144S 591 N.A. 5A2 + A15D 877 N.A. 5A2 + V157N 1163 N.A. 5P + T144V 592 A.A 5A2 + A15D 878 A.A 5A2 + V157N 1164 A.A 5P + T144V 593 N.A. 5A2 + A15E 879 N.A. 5A2 + V157P 1165 N.A. 5P + T144W 594 A.A 5A2 + A15E 880 A.A 5A2 + V157P 1166 A.A 5P + T144W 595 N.A. 5A2 + A15F 881 N.A. 5A2 + V157Q 1167 N.A. 5P + T144Y 596 A.A 5A2 + A15F 882 A.A 5A2 + V157Q 1168 A.A 5P + T144Y 597 N.A. 5A2 + A15G 883 N.A. 5A2 + V157R 1169 N.A. 5P + P157A 598 A.A 5A2 + A15G 884 A.A 5A2 + V157R 1170 A.A 5P + P157A 599 N.A. 5A2 + A15H 885 N.A. 5A2 + V157S 1171 N.A. 5P + P157C 600 A.A 5A2 + A15H 886 A.A 5A2 + V157S 1172 A.A 5P + P157C 601 N.A. 5A2 + A15I 887 N.A. 5A2 + V157T 1173 N.A. 5P + P157D 602 A.A 5A2 + A15I 888 A.A 5A2 + V157T 1174 A.A 5P + P157D 603 N.A. 5A2 + A15K 889 N.A. 5A2 + V157W 1175 N.A. 5P + P157E 604 A.A 5A2 + A15K 890 A.A 5A2 + V157W 1176 A.A 5P + P157E 605 N.A. 5A2 + A15L 891 N.A. 5A2 + V157Y 1177 N.A. 5P + P157F 606 A.A 5A2 + A15L 892 A.A 5A2 + V157Y 1178 A.A 5P + P157F 607 N.A. 5A2 + A15M 893 N.A. 5A2 + Q20K 1179 N.A. 5P + P157G 608 A.A 5A2 + A15M 894 A.A 5A2 + Q20K 1180 A.A 5P + P157G 609 N.A. 5A2 + A15N 895 N.A. 5A2 + V27M 1181 N.A. 5P + P157H 610 A.A 5A2 + A15N 896 A.A 5A2 + V27M 1182 A.A 5P + P157H 611 N.A. 5A2 + A15P 897 N.A. 5A2 + N33K 1183 N.A. 5P + P157I 612 A.A 5A2 + A15P 898 A.A 5A2 + N33K 1184 A.A 5P + P157I 613 N.A. 5A2 + A15Q 899 N.A. 5A2 + V38I 1185 N.A. 5P + P157K 614 A.A 5A2 + A15Q 900 A.A 5A2 + V38I 1186 A.A 5P + P157K 615 N.A. 5A2 + A15R 901 N.A. 5A2 + I56N 1187 N.A. 5P + P157L 616 A.A 5A2 + A15R 902 A.A 5A2 + I56N 1188 A.A 5P + P157L 617 N.A. 5A2 + A15S 903 N.A. 5A2 + D108N 1189 N.A. 5P + P157M 618 A.A 5A2 + A15S 904 A.A 5A2 + D108N 1190 A.A 5P + P157M 619 N.A. 5A2 + A15T 905 N.A. 5A2 + N144T 1191 N.A. 5P + P157N 620 A.A 5A2 + A15T 906 A.A 5A2 + N144T 1192 A.A 5P + P157N 621 N.A. 5A2 + A15V 907 N.A. 5A2 + V27M + A35G 1193 N.A. 5P + P157Q 622 A.A 5A2 + A15V 908 A.A 5A2 + V27M + A35G 1194 A.A 5P + P157Q 623 N.A. 5A2 + A15W 909 N.A. 5A2 + A71G + K75E 1195 N.A. 5P + P157R 624 A.A 5A2 + A15W 910 A.A 5A2 + A71G + K75E 1196 A.A 5P + P157R 625 N.A. 5A2 + A15Y 911 N.A. 5A2 + R11E + L149M 1197 N.A. 5P + P157S 626 A.A 5A2 + A15Y 912 A.A 5A2 + R11E + L149M 1198 A.A 5P + P157S 627 N.A. 5A2 + L18A 913 N.A. 5A2 + R11E + V157P 1199 N.A. 5P + P157T 628 A.A 5A2 + L18A 914 A.A 5A2 + R11E + V157P 1200 A.A 5P + P157T 629 N.A. 5A2 + L18C 915 N.A. 5A2 + D108N + N144T 1201 N.A. 5P + P157V 630 A.A 5A2 + L18C 916 A.A 5A2 + D108N + N144T 1202 A.A 5P + P157V 631 N.A. 5A2 + L18D 917 N.A. 5A2 + L149M + V157D 1203 N.A. 5P + P157W 632 A.A 5A2 + L18D 918 A.A 5A2 + L149M + V157D 1204 A.A 5P + P157W 633 N.A. 5A2 + L18E 919 N.A. 5A2 + L149M + V157P 1205 N.A. 5P + P157Y 634 A.A 5A2 + L18E 920 A.A 5A2 + L149M + V157P 1206 A.A 5P + P157Y 635 N.A. 5A2 + L18F 921 N.A. 3P (5A2 + R11E + 1207 N.A. 5P + I107L L149M + V157P) 636 A.A 5A2 + L18F 922 A.A 3P (5A2 + R11E + 1208 A.A 5P + I107L L149M + V157P) 637 N.A. 5A2 + L18G 923 N.A. 3P + D108N 1209 N.A. 5P + K75E 638 A.A 5A2 + L18G 924 A.A 3P + D108N 1210 A.A 5P + K75E 639 N.A. 5A2 + L18H 925 N.A. 3P + N144T 1211 N.A. 5P + K123E + N156D 640 A.A 5A2 + L18H 926 A.A 3P + N144T 1212 A.A 5P + K123E + N156D 641 N.A. 5A2 + L18I 927 N.A. 3E (5A2 + R11E + 1213 N.A. 5P + I76V L149M + V157E) 642 A.A 5A2 + L18I 928 A.A 3E (5A2 + R11E + 1214 A.A 5P + I76V L149M + V157E) 643 N.A. 5A2 + L18K 929 N.A. 3E + D108N 1215 N.A. 5P + G48D + H57R + L92M + I99V 644 A.A 5A2 + L18K 930 A.A 3E + D108N 1216 A.A 5P + G48D + H57R + L92M + I99V 645 N.A. 5A2 + L18M 931 N.A. 3E + N144T 1217 N.A. 5P + F31L + V36A + I99V 646 A.A 5A2 + L18M 932 A.A 3E + N144T 1218 A.A 5P + F31L + V36A + I99V 647 N.A. 5A2 + L18N 933 N.A. 5P (3P + 1219 N.A. 5P + F31L + H93P D108N + N144T) 648 A.A 5A2 + L18N 934 A.A 5P (3P + 1220 A.A 5P + F31L + H93P D108N + N144T) 649 N.A. 5A2 + L18P 935 N.A. 6P (5P + I56N) 1221 N.A. 5P + V90A 650 A.A 5A2 + L18P 936 A.A 6P (5P + I56N) 1222 A.A 5P + V90A 651 N.A. 5A2 + L18Q 937 N.A. 5E (3E + 1223 N.A. 5P + I44V D108N + N144T) 652 A.A 5A2 + L18Q 938 A.A 5E (3E + 1224 A.A 5P + I44V D108N + N144T) 653 N.A. 5A2 + L18R 939 N.A. 6E (5E + I56N) 1225 N.A. 5P + L46R + H86Q + M106V 654 A.A 5A2 + L18R 940 A.A 6E (5E + I56N) 1226 A.A 5P + L46R + H86Q + M106V 655 N.A. 5A2 + L18S 941 N.A. NLpoly1 1227 N.A. 5P + R141H (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + M106V + L149M + V157D) 656 A.A 5A2 + L18S 942 A.A NLpoly1 1228 A.A 5P + R141H (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + M106V + L149M + V157D) 657 N.A. 5A2 + L18T 943 N.A. NLpoly2 1229 N.A. 5P + N33D + V58A (5A2 + A15S + L18Q + F31I + V58A + A67D + M106V + L149M + V157D) 658 A.A 5A2 + L18T 944 A.A NLpoly2 1230 A.A 5P + N33D + V58A (5A2 + A15S + L18Q + F31I + V58A + A67D + M106V + L149M + V157D) 659 N.A. 5A2 + L18V 945 N.A. NLpoly3 1231 N.A. 5P + I56N + P157H (5A2 + R11N + L18Q + F31I + V58A + A67D + M106V + L149M + V157D) 660 A.A 5A2 + L18V 946 A.A NLpoly3 1232 A.A 5P + I56N + P157H (5A2 + R11N + L18Q + F31I + V58A + A67D + M106V + L149M + V157D) 661 N.A. 5A2 + L18W 947 N.A. NLpoly4 1233 N.A. 5P + L46Q + P157H (5A2 + R11N + A15S + F31I + V58A + A67D + M106V + L149M + V157D) 662 A.A 5A2 + L18W 948 A.A NLpoly4 1234 A.A 5P + L46Q + P157H (5A2 + R11N + A15S + F31I + V58A + A67D + M106V + L149M + V157D) 663 N.A. 5A2 + L18Y 949 N.A. NLpoly5 1235 N.A. 5P + I59V (5A2 + R11N + A15S + L18Q + V58A + A67D + M106V + L149M + V157D) 664 A.A 5A2 + L18Y 950 A.A NLpoly5 1236 A.A 5P + I59V (5A2 + R11N + A15S + L18Q + V58A + A67D + M106V + L149M + V157D) 665 N.A. 5A2 + F31A 951 N.A. NLpoly6 1237 N.A. 5P + A51T + E74K + (5A2 + R11N + A15S + P113L L18Q + F31I + A67D + M106V + L149M + V157D) 666 A.A 5A2 + F31A 952 A.A NLpoly6 1238 A.A 5P + A51T + E74K + (5A2 + R11N + A15S + P113L L18Q + F31I + A67D + M106V + L149M + V157D) 667 N.A. 5A2 + F31C 953 N.A. NLpoly7 1239 N.A. 5P + V36A (5A2 + R11N + A15S + L18Q + F31I + V58A + M106V + L149M + V157D) 668 A.A 5A2 + F31C 954 A.A NLpoly7 1240 A.A 5P + V36A (5A2 + R11N + A15S + L18Q + F31I + V58A + M106V + L149M + V157D) 669 N.A. 5A2 + F31D 955 N.A. NLpoly8 1241 N.A. 5P + A51T (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + L149M + V157D) 670 A.A 5A2 + F31D 956 A.A NLpoly8 1242 A.A 5P + A51T (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + L149M + V157D) 671 N.A. 5A2 + F31E 957 N.A. NLpoly9 1243 N.A. 5P + H57R (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + M106V + V157D) 672 A.A 5A2 + F31E 958 A.A NLpoly9 1244 A.A 5P + H57R (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + M106V + V157D) 673 N.A. 5A2 + F31G 959 N.A. NLpoly10 1245 N.A. 5P + V58A (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + M106V + L149M) 674 A.A 5A2 + F31G 960 A.A NLpoly10 1246 A.A 5P + V58A (5A2 + R11N + A15S + L18Q + F31I + V58A + A67D + M106V + L149M) 675 N.A. 5A2 + F31H 961 N.A. NLpoly11 1247 N.A. 5P + E74K (5A2 + A15S + L18Q + M106V + L149M + V157D) 676 A.A 5A2 + F31H 962 A.A NLpoly11 1248 A.A 5P + E74K (5A2 + A15S + L18Q + M106V + L149M + V157D) 677 N.A. 5A2 + F31I 963 N.A. NLpoly12 1249 N.A. 5P + H86Q (5A2 + A15S + L18Q + A67D + M106V + L149M + V157D) 678 A.A 5A2 + F31I 964 A.A NLpoly12 1250 A.A 5P + H86Q (5A2 + A15S + L18Q + A67D + M106V + L149M + V157D) 679 N.A. 5A2 + F31K 965 N.A. NLpoly13 1251 N.A. 5P + H93P (5A2 + R11N + A15S + L18Q + M106V + L149M + V157D) 680 A.A 5A2 + F31K 966 A.A NLpoly13 1252 A.A 5P + H93P (5A2 + R11N + A15S + L18Q + M106V + L149M + V157D) 681 N.A. 5A2 + F31L 967 N.A. 5P + V 1253 N.A. 5P + I99V 682 A.A 5A2 + F31L 968 A.A 5P + V 1254 A.A 5P + I99V 683 N.A. 5A2 + F31M 969 N.A. 5P + A 1255 N.A. 5P + K123E 684 A.A 5A2 + F31M 970 A.A 5P + A 1256 A.A 5P + K123E 685 N.A. 5A2 + F31N 971 N.A. 5P + VT 1257 N.A. 5P + T128S 686 A.A 5A2 + F31N 972 A.A 5P + VT 1258 A.A 5P + T128S 687 N.A. 5A2 + F31P 973 N.A. 5P + VA 1259 N.A. 5P + L142Q + T154N 688 A.A 5A2 + F31P 974 A.A 5P + VA 1260 A.A 5P + L142Q + T154N 689 N.A. 5A2 + F31Q 975 N.A. 5P + AT 1261 N.A. 5P + H57Q 690 A.A 5A2 + F31Q 976 A.A 5P + AT 1262 A.A 5P + H57Q 691 N.A. 5A2 + F31R 977 N.A. 5P + AA 1263 N.A. 5P + L92M 692 A.A 5A2 + F31R 978 A.A 5P + AA 1264 A.A 5P + L92M 693 N.A. 5A2 + F31S 979 N.A. 5P + GG 1265 N.A. 5P + P113L 694 A.A 5A2 + F31S 980 A.A 5P + GG 1266 A.A 5P + P113L 695 N.A. 5A2 + F31T 981 N.A. 5P + AA 1267 N.A. 5P + G48D 696 A.A 5A2 + F31T 982 A.A 5P + AA 1268 A.A 5P + G48D 697 N.A. 5A2 + F31V 983 N.A. 5P + ATG 1269 N.A. 5P − B9 (−147-157) 698 A.A 5A2 + F31V 984 A.A 5P + ATG 1270 A.A 5P − B9 (−147-157) 699 N.A. 5A2 + F31W 985 N.A. 5P + VTG 1271 N.A. 5P + L46R + P157S 700 A.A 5A2 + F31W 986 A.A 5P + VTG 1272 A.A 5P + L46R + P157S 701 N.A. 5A2 + F31Y 987 N.A. 5P + VTA 1273 N.A. 5P + L46H + P157H 702 A.A 5A2 + F31Y 988 A.A 5P + VTA 1274 A.A 5P + L46H + P157H 703 N.A. 5A2 + V58A 989 N.A. 5P + GTA 1275 N.A. 5P + L46R + H93P 704 A.A 5A2 + V58A 990 A.A 5P + GTA 1276 A.A 5P + L46R + H93P 705 N.A. 5A2 + V58C 991 N.A. 5P + VTGW 1277 N.A. 5P + L46R + H93P + F31L 706 A.A 5A2 + V58C 992 A.A 5P + VTGW 1278 A.A 5P + L46R + H93P + F31L 707 N.A. 5A2 + V58D 993 N.A. 5P + VTGWR 1279 N.A. 5P + L46R + H93P + K75E 708 A.A 5A2 + V58D 994 A.A 5P + VTGWR 1280 A.A 5P + L46R + H93P + K75E 709 N.A. 5A2 + V58E 995 N.A. 5P + VTGWE 1281 N.A. 5P + L46R + H93P + I76V 710 A.A 5A2 + V58E 996 A.A 5P + VTGWE 1282 A.A 5P + L46R + H93P + I76V 711 N.A. 5A2 + V58F 997 N.A. 5P + VTGWK 1283 N.A. 8S (5P + L46R + H93P + P157S + F31L) 712 A.A 5A2 + V58F 998 A.A 5P + VTGWK 1284 A.A 8S (5P + L46R + H93P + P157S + F31L) 713 N.A. 5A2 + V58G 999 N.A. 5P + VTGWQ 1285 N.A. 5P + L46R + H93P + P157S + K75E 714 A.A 5A2 + V58G 1000 A.A 5P + VTGWQ 1286 A.A 5P + L46R + H93P + P157S + K75E 715 N.A. 5A2 + V58H 1001 N.A. 5P + VTGWH 1287 N.A. 5P + L46R + H93P + P157S + I76V 716 A.A 5A2 + V58H 1002 A.A 5P + VTGWH 1288 A.A 5P + L46R + H93P + P157S + I76V 717 N.A. 5A2 + V58I 1003 N.A. 5P D1 (−157) 1289 N.A. 12S (8S + A51T + K75E + I76V + I107L) 718 A.A 5A2 + V58I 1004 A.A 5P D1 (−157) 1290 A.A 12S (8S + A51T + K75E + I76V + I107L) 719 N.A. 5A2 + V58K 1005 N.A. 5P D2 (−156-157) 1291 N.A. 11S (12 − A51T) 720 A.A 5A2 + V58K 1006 A.A 5P D2 (−156-157) 1292 A.A 11S (12 − A51T) 721 N.A. 5A2 + V58L 1007 N.A. 5P D3 (−155-157) 1293 N.A. 12S − K75E 722 A.A 5A2 + V58L 1008 A.A 5P D3 (−155-157) 1294 A.A 12S − K75E 723 N.A. 5A2 + V58M 1009 N.A. 5P D4 (−154-157) 1295 N.A. 12S − I76V 724 A.A 5A2 + V58M 1010 A.A 5P D4 (−154-157) 1296 A.A 12S − I76V 725 N.A. 5A2 + V58N 1011 N.A. 5P D5 (−153-157) 1297 N.A. 12S − I107L 726 A.A 5A2 + V58N 1012 A.A 5P D5 (−153-157) 1298 A.A 12S − I107L

The polypeptides and coding nucleic acid sequences of Table 2 (SEQ ID NOS: 441-1298) all contain N-terminal Met residues (amino acids) or ATG start codons (nucleic acids). In some embodiments, the polypeptides and coding nucleic acid sequences of Table 2 are provided without N-terminal Met residues or ATG start codons (SEQ ID NOS: 1299-2156).

In certain embodiments, an internal tag and/or structural complement comprises one of the amino acid polymers of SEQ ID NOS: 441-2156. In some embodiments, an internal tag and/or structural complement comprises a single amino acid difference from SEQ ID NO: 440.

In some embodiments, an internal tag and/or structural complement comprises two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 . . . 35 . . . 40 . . . 45 . . . 50, or more) amino acid differences from SEQ ID NO: 440 and/or any of the amino acid polymers of SEQ ID NOS:441-2156. In some embodiments, an internal tag and/or structural complement are provided comprising the sequence of one of the amino acid polymers of SEQ ID NOS: 441-2156 with one or more additions, substitutions, and/or deletions. In some embodiments, an internal tag and/or structural complement or a portion thereof comprises greater than 70% sequence identity (e.g., >71%, >75%, >80%, >85%, >90%, >91%, >92%, >93%, >94%, >95%, >96%, >97%, >98%, or >99%) with one or more of the amino acid polymers of SEQ ID NOS: 441-2156.

In certain embodiments, a nucleic acid from Table 2 is provided. In some embodiments, a nucleic acid encoding a polypeptide from Table 2 (e.g., inserted into a polypeptide of interest) is provided. In some embodiments, a nucleic acid of the present invention codes for a polypeptide that comprises a single amino acid difference from SEQ ID NO: 440 and/or any of the amino acid polymers of SEQ ID NOS: 441-2156 (e.g., inserted into a polypeptide of interest). In some embodiments, nucleic acids code for a polypeptide comprising two or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 . . . 35 . . . 40 . . . 45 . . . 50, or more) amino acid differences from SEQ ID NO: 440 and/or any of the polypeptides listed in Table 2 (e.g., inserted into a polypeptide of interest). In some embodiments, nucleic acids are provided comprising the sequence of one of the nucleic acid polymers of SEQ ID NOS: 441-2156 (e.g., inserted into a polypeptide of interest). In some embodiments, nucleic acids are provided comprising the sequence of one of the nucleic acid polymers of SEQ ID NOS: 441-2156 with one or more additions, substitutions, and/or deletions. In some embodiments, a nucleic acid or a portion thereof comprises greater than 70% sequence identity (e.g., >71%, >75%, >80%, >85%, >90%, >91%, >92%, >93%, >94%, >95%, >96%, >97%, >98%, or >99%) with one or more of the nucleic acid polymers of SEQ ID NOS: 441-2156 (e.g., inserted into a polypeptide of interest). In some embodiments, a nucleic acid or a portion thereof codes for an polypeptide comprising greater than 70% sequence identity (e.g., >71%, >75%, >80%, >85%, >90%, >91%, >92%, >93%, >94%, >95%, >96%, >97%, >98%, or >99%) with one or more of the amino acid polymers of SEQ ID NOS: 441-2156 (e.g., inserted into a polypeptide of interest). In some embodiments, nucleic acids are provided that code for one of the polypeptides of SEQ ID NOS: 441-2156 (e.g., inserted into a polypeptide of interest). In some embodiments, nucleic acids are provided that code for one of the polypeptides of SEQ ID NOS: 441-2156 with one or more additions, substitutions, and/or deletions (e.g., inserted into a polypeptide of interest).

The present invention provides compositions and methods that are useful in a variety of fields including basic research, medical research, molecular diagnostics, etc. The reagents and assays described herein are not limited to any particular applications, and any useful application should be viewed as being within the scope of the present invention.

Typical applications that make use of embodiments of the present invention involve the monitoring/detection of protein-protein interactions (e.g., heterodimers, homodimers) (See FIG. 1), protein-RNA interactions, protein-DNA interactions, protein-small molecule interactions, or any other combinations of molecular entities. A protein of interest is internally tagged and the second entity of interest is attached to the structural complement. If a detectable signal is produced under the particular assay conditions, then interaction of the protein of interest and the entity of interest is inferred. Such assays are useful for monitoring molecular interactions under any suitable conditions (e.g., in vitro, in vivo, in situ, whole animal, etc.), and find use in, for example, drug discovery, elucidating molecular pathways, studying equilibrium or kinetic aspects of complex assembly, high throughput screening, proximity sensor, etc.

Other typical applications that make use of embodiments of the present invention involve the detection or localization (e.g., cellular localization, subcellular localization, etc.) of a protein or polypeptide (See FIG. 2). A protein of interest in a sample is internally tagged, and a structural complement is added to the sample. If a detectable signal is produced under the particular assay conditions, then the presence or location of the protein of interest is inferred. Such assays are useful for detecting or localizing a protein under any suitable conditions (e.g., in vitro, in vivo, in situ, whole animal, etc.), and find use in, for example, drug discovery, elucidating molecular pathways, studying equilibrium or kinetic aspects of complex assembly, high throughput screening, proximity sensor, etc.

In some embodiments, an internal tag and structural complement of known characteristics (e.g., spectral characteristics, mutual affinity of pair) is used to elucidate the affinity of, or understand the interaction of, a protein of interest and a potentially associated entity of interest (protein, nucleic acid, small molecule, etc.). In other embodiments, a well-characterized interaction pair is used to determine the characteristics (e.g., spectral characteristics, mutual affinity of pair) of an internal tag and structural complement.

Embodiments described herein find use in drug screening and/or drug development. For example, the interaction of a small molecule drug or an entire library of small molecules (e.g., labeled with structural complement) with an internally tagged target protein of interest (e.g., therapeutic target) is monitored under one or more relevant conditions (e.g., physiological conditions, disease conditions, etc.). In other embodiments, the ability of a small molecule drug or an entire library of small molecules to enhance or inhibit the interactions between two entities (e.g., receptor and ligand, protein-protein, etc.) is assayed. In some embodiments, drug screening applications are carried out in a high through-put format to allow for the detection of the binding of tens of thousands of different molecules to a target, or to test the effect of those molecules on the binding of other entities.

In some embodiments, the present invention provides the detection of molecular interactions in living organisms (e.g., bacteria, yeast, eukaryotes, mammals, primates, human, etc.) and/or cells. In some embodiments, internally tagged protein and complement-labeled protein are co-expressed in the cell or whole organism, and signal is detected and correlated to the formation of the interaction complex. In some embodiments, cells are transiently and/or stably transformed or transfected with vector(s) (e.g., encoding internally-tagged protein, complement-labeled protein, etc.). In some embodiments, transgenic organisms are generated that code for the necessary components (e.g., internally-tagged protein, complement-labeled protein, etc.) for carrying out the assays described herein. In other embodiments, vectors are injected into whole organisms.

The present invention also provides methods for the design and/or optimization of internal tags and structural complements and the bioluminescent complexes that form therefrom. Any suitable method for the design of non-luminescent pairs/groups that are consistent with embodiments described herein, and/or panels thereof, is within the scope of the present invention.

EXPERIMENTAL Example 1

Experiments were conducted during development of embodiments of the present invention to demonstrate structural complementation between the non-luminescent polypeptide, NLpoly11S and the high affinity, non-luminescent peptide, NLpep86, as an experimental model. HALOTAG was selected as the target for insertion of the NLpep86. A number of HALOTAG—NLpep86 fusion proteins were generated by inserting a tandem of NLpep86 (high affinity, sequence GSSG-[VSGWRLFKKIS]-E-[VSGWRLFKKIS]-GSSG (SEQ ID NO: 2580)) at various sites within the HALOTAG protein (insertion sites: 18/19, 32/33, 78/79, 98/99). Initial experiments were performed in HeLa cells transiently transfected with NLpoly11S and the indicated HALOTAG-NLpep86 fusion proteins. The results show that it is possible to achieve structural complementation between NLpoly11S and NLpep86 inserted at different positions within HALOTAG (FIG. 4). HALOTAG function was determined by BRET (which requires the ability of modified HALOTAG to bind HALOTAG ligand, FIG. 4) or imaging of TMR-HT ligand labeled cells (FIG. 5). It was demonstrated that insertion of NLpep86 is compatible with HALOTAG function (FIG. 5). The observed efficiency of structural complementation using internal fusions varies between 1-40% relative to N- or C-terminal NLpep86 fusions to HALOTAG using NLpoly11S and NLpep86.

Example 2

Experiments were conducted to demonstrate test antibody driven NANOLUC bioluminescence complementation using an NLpep114 internally tagged target protein and an NLpoly11S tagged protein G.

Construction, Expression, and Purification of Protein G-11S

ATG-2071 (NLpoly11S-tagged protein G) plasmid (SEQ ID NO: 2576): Amino acids 303-497 from Immunoglobulin G-binding protein G [Uniprot P19909] were amplified from a synthetic gene (GenScript) to add a 6×His tag and cloned into pF5K (Flexi vector, CMV promoter) containing linker-NLpoly11S. The 6×His-proteinG-NLpoly11S fusion was then subcloned into pF1A (Flexi vector, T7 promoter; Promega) for bacterial expression.

NLpoly11S-tagged protein G was produced in an E. coli expression system by the Glucose/Rhamnose Auto-Induction Method. Briefly, plasmid ATG-2071 was transformed into E. coli KRX cells (Promega) using the manufacturer's recommended protocol and grown 17-22 hrs at 37° C. with shaking (275 rpm) in LB media (50 ml) containing antibiotic. This starter culture was diluted (1:100) into 250 ml of auto-induction media (LB media with glucose and rhamnose (0.05% each) and antibiotic) and grown 17-22 hrs at 25° C. with shaking (275 rpm). Cells were collected by centrifugation (5,000×g for 20 min at 4° C.), the media removed, and the bacterial cell pellet stored at −20° C.

Pelleted cells were re-suspended in 50 ml Lysis Buffer (100 mM HEPES (pH 7.5), 500 mM NaCl, 10 mM Imidazole, 0.5× FastBreak (Promega), 1× Protease Inhibitor Cocktail (Promega), 0.2 mg/ml lysozyme (Sigma) and 250 units of RQ1 DNase (Promega)), and then incubated at ambient temperature for 30 min with occasional mixing. The soluble fraction was separated by centrifugation (15,000×g for 20 min at 4° C.) and applied (1 ml/min) to a 5 ml HisTrap column (Life Technologies) equilibrated with Start Buffer (50 mM HEPES (pH 7.5), 500 mM NaCl, 10 mM Imidazole). After sample application, the resin was washed with 4 CVs Start Buffer. Bound protein was eluted with a 20 CV linear gradient, 0-100% Limit Buffer (50 mM HEPES (pH 7.5), 500 mM Imidazole). Fractions (2.5 ml) were analyzed by SDS/PAGE. Those with significant amounts of a major 41 kDa band (NLpoly11S/pG) and minimal contaminants were pooled and dialyzed against 1×PBS and stored at −20° C.

Methods for Expression Plasmid Construction for VEGFA Constructs

VEGF constructs ATG-1915 (SEQ ID NO: 2577), -1917 (SEQ ID NO: 2578) and -1946 (SEQ ID NO: 2579) were built by transferring VEGFA-165 fused to either NLpep114 and/or FLAG octapeptide (both synthetic genes; Gene Dynamics) into the vector pCIHN (Flexi vector, CMV promoter; Promega). This vector contains an N-terminal HALOTAG—with an IL6 secretion signal.

General Cell Transfection Protocol

NLpep114-target fusion construct DNA was diluted into carrier DNA (pGEM3Zf(−); Promega) at bug total DNA at a mass ratio of 1:10. DNA:FuGENE complexes were formed at a ratio of 1:3 (ug DNA/ul FuGENE), according to manufacturer's protocol (Promega). One part of the transfection complex was mixed with 20 parts (volume/volume) of HEK293T cells (ATCC) suspended at a density of 2×10⁵ cells/ml in DMEM (Gibco)+10% FBS (Hyclone). Cells (50 ul/well) were dispensed into 96-well tissue culture plates and incubated in a humidified, 37° C./5% CO₂ incubator for 18-24 hours.

Target Antibody Driven NANOLUC Bioluminescence Complementation

HEK293T cells (ATCC) were transfected with three NLpep114-VEGFA DNAs as described above and incubated overnight. The cells were serum starved for 4 hours under the same conditions by replacing the media with an equal volume of (Gibco). NLpoly11S(15)pG in 1×PBS/0.1% BSA (Promega) was added (25 ul/well) to a final concentration of 0.5 ug/ml (12 nM). Anti-VEGF antibody (R&D Systems, #293) in 1×PBS/0.1% BSA (Promega) was added (25 ul/well) to a final concentration of 0-0.73 ug/ml (0-5.3 nM). After the addition of LCS Reagent (Promega, 100 ul/well, 10 μM final concentration), luciferase activity was measured using an Infinity F500 microtiter plate reader (Tecan).

FIGS. 6-11 demonstrate that when incubated together, the NLpep114-VEGF fusion protein, the NLpoly11S-protein G fusion protein, and the un-modified anti-VEGF antibody come together to form an active luciferase complex. The signal is measurable, but extremely low in the absence of antibody. Given the high K_(D) of the NLpoly11S/NLpep114 interaction, non-facilitated complementation should be extremely low at the concentrations used. This indicates that the NLpoly11S fragment has some low level of residual luciferase activity. For ATG-1915 (HT-VEGF-114), this background signal increased by over 400-fold as the anti-VEGF antibody concentration increased from 0-0.73 ug/ml (0-5.3 nM).

The context of the NLpep114 tag influences the overall system performance. ATG-1915 with a C-terminal (external) NLpep114 tag has the highest signal. This construct suffers a 40% signal loss when the NLpep114 tag is slightly internalized by the addition of a C-terminal FLAG sequence (ATG-1946). When placed between two large domains, the signal is reduced 5-fold (ATG-1917). Note that while the total signal varies with the position of the NLpep114 tag, the calculated EC₅₀ remains constant. The context of the NLpep114 tag changes the level of complementation, but not the affinity of the NLpoly 11 S/NLpep114 pair.

Example 3

Experiments were conducted to demonstrate facilitated NANOLUC bioluminescence complementation using the binding pair, FKBP and Frb (FIG. 13).

All transfections were performed as reverse transfections by mixing the transfection complex with a suspension of cells prior to plating. Briefly, a transfection mix (sufficient for one 96-well plate) was made containing 500 ul OptiMEM, 5 ug DNA, and 15 uL Fugene HD (Promega). The DNA of the complementation pair (Frb-X/FKBP-Y) was at a ratio of 1:1

For the transfection, the DNA of the complementation pair was used either un-diluted or at a dilution of 1:50. Total DNA content was adjusted to 5 ug using pGEM3Z as carrier DNA.

The transfection mix was mixed by gentle vortexing and incubated for 5-10 min at room temperature prior to use.

Cells were harvested by trypsination, washed, and diluted to a concentration of 2×10⁵ cells/ml in DMEM+10% FBS. For the transfection, 0.5 ml transfection mix was added to 10 ml of cell suspension. The cell suspension was then plated into wells of a white, 96-well tissue culture plate (100 uL per well) and incubated 0/N at 37° C.

Three different assays were performed on the transfected cells.

-   -   a) Endpoint assay using a single concentration of Rapamycin         (FIGS. 14 and 15)         -   Growth medium (DMEM+10% FBS) on the transfected cells was             removed by aspiration, and 100 uL OptiMEM including             Rapamycin (1 mM) and furimazine (10 mM) was added. The cells             were incubated for 10 minutes at room temperature, and             luminescence read on BMG Clariostar or Glomax Multi plus             plate reader.     -   b) Endpoint assay—Rapamycin dose response (FIG. 16)         -   Growth medium (DMEM+10% FBS) on the transfected cells was             removed by aspiration, and 100 uL OptiMEM including a serial             dilution of Rapamycin and furimazine (10 mM) was added. The             cells were incubated for 10 minutes at room temperature, and             luminescence read on BMG Clariostar or Glomax Multi plus             plate reader.     -   c) Kinetic assay (FIGS. 17 and 18)         -   Growth medium (DMEM+10% FBS) on the transfected cells was             removed by aspiration, and 50 uL OptiMEM including             furimazine (10 mM) was added. Luminescence detection was             initiated on a BMG Clariostar plate reader, and 50 uL             OptiMEM including Rapamycin (1 mM) and furimazine (10 mM)             was injected onto the cells. Luminescence was continuously             read.

Example 4

Internal High-Affinity NLpep finds use in a variety of embodiments. Cases arise in which neither the N-terminus nor the C-terminus represent attractive points for attachment of a protein tag. For example,

1) The protein terminus is not in the desired cellular localization. For instance, for a given membrane protein, it may be desired to have the tag on the extracellular side, but both termini are intracellular.

2) Terminal addition of a tag interrupts protein-protein interactions. For instance, many membrane proteins (such as ADRB2) have PDZ-binding motifs at their very C-terminus. Addition of a C-terminal tag would abolish these interactions and alter proper protein functioning.

3) It is desired for the tag to be placed spatially closer to a given site on the protein than the terminus allows.

4) N-terminal tag placement disrupts proper signal sequence function and cleavage.

5) The termini is already used for other tags or fusion proteins.

Example 5

Internal High-Affinity NLpep finds use in the measurement of surface expression of membrane proteins. It is commonly desired to measure the amount of a given protein expressed on the cell surface. This enables studies of:

-   -   Receptor activation and internalization     -   Receptor recycling from endosomes     -   Regulated exocytosis     -   Protein trafficking and secretion

In some embodiments, the following experiments are configured so that purified an NLpoly, e.g., NLpoly11S, protein plus furimazine substrate can be added to the extracellular medium. Complementation with a high-affinity NLpep sequence, e.g., NLpep80, on the extracellular side of the plasma membrane can lead to spontaneous complementation, giving a luminescent signal that is directly proportional to the amount of protein on the surface.

a) The F508del mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) is the most common cause of cystic fibrosis, and it prevents the protein from being correctly targeted to the plasma membrane, so it is instead degraded. Small molecule chaperones have been identified that can promote increased trafficking to the surface. To screen for such small molecules, it is beneficial to have a simple luminescent assay for quantifying surface expression of CFTR.

Tagging CFTR with the high-affinity NLpep allows quantification of surface expression, but both the N- and C-termini of CFTR are intracellular. Therefore, the NLpep tag is placed in one of the extracellular loops of the protein. In some embodiments, a Flag epitope tag is placed after residue Asn901 previously to provide an extracellular tag. Insertion of the high-affinity NLpep sequence at the same location in the F508del variant of CFTR allows one or more of the following:

-   -   1) Simple quantification of the amount of protein at the plasma         membrane. Cells could be treated with compound libraries and         positive control compounds known to promote proper trafficking,         and the luminescence measured with live cells in the presence of         a NLpoly, e.g., NLpoly11S, plus furimazine.     -   2) The cells are treated with a lytic reagent containing a         NLpoly, e.g., NLpoly11S, plus furimazine in order to quantify         the total amount of protein in the cell. Reduced protein         degradation would increase the luminescent signal.     -   3) The glycosylation of CFTR that occurs during its maturation         is easily detected as band shifting on a protein blot by         addition of a NLpoly, e.g., NLpoly11S, plus furimazine in buffer         to the blot membrane.

b) The trafficking of neurotransmitter receptors in and out of the plasma membrane is tightly regulated. AMPA receptors (AMPARs) mediate fast excitatory synaptic transmission, and synaptic strength is determined by the composition of AMPARs in the postsynaptic membrane, which is controlled by regulated trafficking of AMPAR subunits. Insertion of high-affinity NLpep into extracellular loops of AMPA receptors allows for straightforward measurement of protein levels and the kinetics of exocytosis and endocytosis.

All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in the relevant fields are intended to be within the scope of the present invention. 

We claim:
 1. A method for detecting a stable interaction between a first amino acid sequence and a second amino acid sequence comprising: (a) placing (i) an internal fusion comprising an N-terminal segment of a first amino acid sequence of interest, a C-terminal segment of the first amino acid sequence of interest, and an internal tag between the N-terminal and C-terminal segments, wherein the internal tag comprises an amino acid sequence having less than 100% and greater than 45% sequence identity with SEQ ID NO: 2 inserted within the first amino acid sequence of interest, (ii) a second fusion comprising a second amino acid sequence of interest and an amino acid sequence having less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, and (iii) a furimazine or coelenterazine substrate in conditions that allow for a possible stable interaction to occur between the first amino acid sequence of interest and the second amino acid sequence of interest, wherein a bioluminescent signal produced in the presence of a furimazine or coelenterazine substrate is substantially increased when the internal tag contacts the amino acid sequence having less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, when compared to a bioluminescent signal produced in the presence of the substrate but in the absence of contact between the internal tag and the amino acid sequence having less than 100% and greater than 45% sequence identity with SEQ ID NO: 440; and (b) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates a stable interaction between the first amino acid sequence of interest and the second amino acid sequence of interest.
 2. The method of claim 1, wherein said second fusion is an internal fusion or a traditional fusion.
 3. The method of claim 1, wherein the first internal fusion is expressed from a first nucleic acid sequence and the second fusion is expressed from a second nucleic acid sequence.
 4. The method of claim 3, wherein a single vector comprises the first nucleic acid sequence and the second nucleic acid sequence.
 5. The method of claim 3, wherein the first nucleic acid sequence and the second nucleic acid sequence are on separate vectors.
 6. The method of claim 3, wherein steps (a) and (b) comprise expressing the internal fusion and second fusion within a cell.
 7. A method for detecting a stable interaction between a first amino acid sequence and a second amino acid sequence comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2; (b) creating a second fusion of the second amino acid sequence and a complement peptide, wherein the complement peptide has less than 100% and greater than 45% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the complement peptide contacts a polypeptide of SEQ ID NO: 440; (c) placing the internal fusion, second fusion, and a coelenterazine substrate in conditions that allow for a possible stable interaction to occur between the first amino acid sequence and the second amino acid sequence to; and (d) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates a stable interaction between the first amino acid sequence and the second amino acid sequence.
 8. The method of claim 7, wherein said second fusion is an internal fusion or a traditional fusion.
 9. The method of claim 7, wherein the internal fusion is expressed from a first nucleic acid sequence coding for the first amino acid sequence and the internal tag, and the second fusion is expressed from a second nucleic acid sequence coding for the second amino acid sequence and the complement peptide.
 10. The method of claim 9, wherein a single vector comprises the first nucleic acid sequence and the second nucleic acid sequence.
 11. The method of claim 9, wherein the first nucleic acid sequence and the second nucleic acid sequence are on separate vectors.
 12. The method of claim 9, wherein step (a) comprises expressing the internal fusion and second fusion within a cell.
 13. A method comprising providing a polypeptide for use in an assay, the polypeptide comprising an N-terminal segment of a protein of interest, a C-terminal segment of a protein of interest, and an internal tag between the N-terminal and C-terminal segments, wherein the internal tag comprises an amino acid sequence having less than 100% and greater than 45% sequence identity with SEQ ID NO: 2 inserted within the protein of interest; wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide consisting of SEQ ID NO: 440 wherein the polypeptide is not a naturally occurring polypeptide.
 14. The method of claim 13, for detecting a target polypeptide in a sample comprising: (a) creating an internal fusion by inserting an internal tag into the target polypeptide, such that said internal tag is neither at the N-terminus not the C-terminus of the target polypeptide, wherein the internal tag has less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2; (b) adding to said sample: (i) a complement peptide that has less than 100% and greater than 45% sequence identity with SEQ ID NO: 2, and (ii) a coelenterazine substrate; (c) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates the presence of the target polypeptide in the sample.
 15. The method of claim 14, wherein the sample comprises a cell.
 16. The method of claim 15, wherein step (a) comprises expressing said internal fusion in said cell.
 17. The method of claim 16, wherein step (b)(i) comprises expressing said complement peptide in said cell.
 18. The method of claim 13, for detecting a target polypeptide in a sample comprising: (a) creating an internal fusion by inserting an internal tag into the target polypeptide, such that said internal tag is neither at the N-terminus not the C-terminus of the target polypeptide, wherein the internal tag has less than 100% and greater than 45% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 440; (b) adding to said sample: (i) a complement polypeptide that has less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, and (ii) a coelenterazine substrate; (c) detecting, if present, a bioluminescent signal emitted, wherein detection of the bioluminescent signal indicates the presence of the target polypeptide in the sample.
 19. The method of claim 18, wherein the sample comprises a cell.
 20. The method of claim 19, wherein step (a) comprises expressing said internal fusion in said cell.
 21. The method of claim 19, wherein step (b)(i) comprises said complement polypeptide in said cell.
 22. The method of claim 13, for detecting alteration of an interaction between a first amino acid sequence and a second amino acid sequence by a potential inhibitory agent comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 45% sequence identity with SEQ ID NO: 2, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide of SEQ ID NO: 440; (b) creating a second fusion of the second amino acid sequence and a complement polypeptide, wherein the complement polypeptide has less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, and wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the complement polypeptide contacts a peptide of SEQ ID NO: 2; (c) placing the internal fusion, second fusion, and a coelenterazine substrate in conditions that allow for a possible stable interaction to occur between the first amino acid sequence and the second amino acid sequence; (d) detecting, if present, a bioluminescent signal emitted; wherein detection of the bioluminescent signal indicates a stable interaction between the first amino acid sequence and the second amino acid sequence; (e) adding the potential inhibitory agent to the internal fusion, second fusion, and a coelenterazine substrate; (f) detecting, if present, a bioluminescent signal emitted; and (g) comparing the bioluminescent signals of steps (d) and (f), wherein decrease in bioluminescent signal from step (d) to step (f) indicates inhibition of the interaction between the first amino acid sequence and the second amino acid sequence by the potential inhibitory agent.
 23. The method of claim 22, wherein steps (a) and (b) comprise expressing the internal fusion and second fusion within a cell.
 24. The method of claim 22, wherein the potential inhibitory agent is a peptide or small molecule.
 25. The method of claim 13, for determining the structural conformation of a first amino acid sequence comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 45% sequence identity with SEQ ID NO: 2, wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a polypeptide of SEQ ID NO: 440, wherein a first structural conformation of the first amino acid sequence prevents access to the internal tag, and wherein a second structural conformation of the first amino acid sequence allows access to the internal tag; (b) placing the internal fusion and either (i) a complement polypeptide having less than 100% and greater than 45% sequence identity with SEQ ID NO: 440 or (ii) a second fusion of a second amino acid sequence and the complement polypeptide in the presence of a coelenterazine substrate; (c) detecting, if present, a bioluminescent signal emitted, wherein absence of the bioluminescent signal indicates the first amino acid sequence is adopting the first structural conformation, and wherein presence of the bioluminescent signal indicates the first amino acid sequence is adopting the second structural conformation.
 26. The method of claim 25, wherein step (c) comprises: (i) detecting, if present, a bioluminescent signal emitted wherein the absence of the bioluminescent signal indicates the first amino acid sequence is adopting the first structural conformation; (ii) inducing a conformational change in the first amino acid sequence; and (iii) detecting, if present, a bioluminescent signal emitted wherein the presence of the bioluminescent signal indicates the first amino acid sequence is adopting the second structural conformation.
 27. The method of claim 26, wherein inducing a conformational change is selected from: adding a protease that cleave a portion of the first amino acid sequence, addition an agent that binds to the first amino acid sequence, and altering the assay conditions.
 28. The method of claim 13, for determining the structural conformation of a first amino acid sequence comprising: (a) creating an internal fusion by inserting an internal tag into the first amino acid sequence, such that said internal tag is neither at the N-terminus not the C-terminus of the first amino acid sequence, wherein the internal tag has less than 100% and greater than 45% sequence identity with SEQ ID NO: 440, wherein a detectable bioluminescent signal is produced in the presence of a coelenterazine substrate when the internal tag contacts a peptide of SEQ ID NO: 2, wherein a first structural conformation of the first amino acid sequence prevents access to the internal tag, and wherein a second structural conformation of the first amino acid sequence allows access to the internal tag; (b) placing the internal fusion and either (i) a complement peptide having less than 100% and greater than 45% sequence identity with SEQ ID NO: 2 or (ii) a second fusion of a second amino acid sequence and the complement peptide in the presence of a coelenterazine substrate; (c) detecting, if present, a bioluminescent signal emitted, wherein absence of the bioluminescent signal indicates the first amino acid sequence is adopting the first structural conformation, and wherein presence of the bioluminescent signal indicates the first amino acid sequence is adopting the second structural conformation.
 29. The method of claim 28, wherein step (c) comprises: (i) detecting, if present, a bioluminescent signal emitted wherein the absence of the bioluminescent signal indicates the first amino acid sequence is adopting the first structural conformation; (ii) inducing a conformational change in the first amino acid sequence; and (iii) detecting, if present, a bioluminescent signal emitted wherein the presence of the bioluminescent signal indicates the first amino acid sequence is adopting the second structural conformation.
 30. The method of claim 29, wherein inducing a conformational change is selected from: adding a protease that cleave a portion of the first amino acid sequence, addition an agent that binds to the first amino acid sequence, and altering the assay conditions. 